<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD Journal Publishing with OASIS Tables v3.0 20080202//EN" "journalpub-oasis3.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" xml:lang="en" dtd-version="3.0"><?xmltex \bartext{Earth Observation for Integrated Water and Basin Management: Challenges for adaptation to a changing environment}?>
  <front>
    <journal-meta><journal-id journal-id-type="publisher">PIAHS</journal-id><journal-title-group>
    <journal-title>Proceedings of the International Association of Hydrological Sciences</journal-title>
    <abbrev-journal-title abbrev-type="publisher">PIAHS</abbrev-journal-title><abbrev-journal-title abbrev-type="nlm-ta">Proc. IAHS</abbrev-journal-title>
  </journal-title-group><issn pub-type="epub">2199-899X</issn><publisher>
    <publisher-name>Copernicus Publications</publisher-name>
    <publisher-loc>Göttingen, Germany</publisher-loc>
  </publisher></journal-meta>
    <article-meta>
      <article-id pub-id-type="doi">10.5194/piahs-380-73-2018</article-id><title-group><article-title>Use of Sentinel 2 – MSI for water quality monitoring at Alqueva reservoir, Portugal</article-title><alt-title>Earth Observation for Integrated Water and Basin Management</alt-title>
      </title-group><?xmltex \runningtitle{Earth Observation for Integrated Water and Basin Management}?><?xmltex \runningauthor{M. Potes et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>Potes</surname><given-names>Miguel</given-names></name>
          <email>mpotes@uevora.pt</email>
        <ext-link>https://orcid.org/0000-0002-8912-5277</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Rodrigues</surname><given-names>Gonçalo</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Penha</surname><given-names>Alexandra Marchã</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Novais</surname><given-names>Maria Helena</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Costa</surname><given-names>Maria João</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-2981-2232</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff2">
          <name><surname>Salgado</surname><given-names>Rui</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-1311-6291</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1 aff3">
          <name><surname>Morais</surname><given-names>Maria Manuela</given-names></name>
          
        </contrib>
        <aff id="aff1"><label>1</label><institution>Institute of Earth Sciences – ICT, IIFA, University of Évora,
Évora, 7000-671, Portugal</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>Department of Physics, ECT, University of Évora, Évora,
7000-671, Portugal</institution>
        </aff>
        <aff id="aff3"><label>3</label><institution>Department of Biology, ECT, University of Évora, Évora,
7000-671, Portugal</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Miguel Potes (mpotes@uevora.pt)</corresp></author-notes><pub-date><day>18</day><month>December</month><year>2018</year></pub-date>
      
      <volume>380</volume>
      <fpage>73</fpage><lpage>79</lpage>
      <history>
        <date date-type="received"><day>18</day><month>April</month><year>2018</year></date>
           <date date-type="rev-recd"><day>10</day><month>July</month><year>2018</year></date>
           <date date-type="accepted"><day>27</day><month>July</month><year>2018</year></date>
      </history>
      <permissions>
        
        
      <license license-type="open-access"><license-p>This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/4.0/">https://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><self-uri xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018.html">This article is available from https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018.html</self-uri><self-uri xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018.pdf">The full text article is available as a PDF file from https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018.pdf</self-uri>
      <abstract>
    <p id="d1e144">Alqueva reservoir located in southeast of Portugal has a surface area of
250 km<inline-formula><mml:math id="M1" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula> and total capacity of 4150 hm<inline-formula><mml:math id="M2" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula>. Since 2006 the water
quality of this reservoir is explored by the authors using remote sensing
techniques. First using MERIS multi-spectral radiometer on-board of ENVISAT-1
and presently with MSI multi-spectral radiometer on-board SENTINEL-2. The
existence of two satellites (A and B) equipped with MSI enable the area to be
revisited, under the same viewing conditions, every 2–3 days. Since 2017 the
multidisciplinary project ALOP (ALentejo Observation and Prediction systems)
expands the team knowledge about the physical and bio-chemical properties of
the reservoir. This project includes an integrated field campaign at
different experimental sites in the reservoir and its shores, at least until
September 2018. Previous algorithms developed by the team for MERIS are
tested with the new MSI instrument for water turbidity, chlorophyll <inline-formula><mml:math id="M3" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>
concentration and density of cyanobacteria. Results from micro-algae bloom
occurred in late summer/early autumn 2017 on the reservoir are presented,
showing the capabilities of MSI sensor for detection and high resolution
mapping over the reservoir. The results are compared with in situ sampling
and laboratorial analysis of chlorophyll <inline-formula><mml:math id="M4" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> associated with the bloom.</p>
  </abstract>
    </article-meta>
  </front>
<body>
      

<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p id="d1e186">The water quality monitoring of inland reservoirs is essential to ensure that
it remains within acceptable boundaries or otherwise, to trigger actions that
may revert the water quality degradation. The set-up of early warning systems
is important for reservoirs, which may be affected by pollution events,
alerting the authorities to water quality degradation episodes. The Alqueva
reservoir, located in southwestern Iberian Peninsula (south of Portugal), has
a total capacity of 4.150 hm<inline-formula><mml:math id="M5" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> and a surface area of 250 km<inline-formula><mml:math id="M6" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>,
constituting the largest reservoir in the Iberian Peninsula. It is a
multi-purpose structure used for water supply, irrigation, hydroelectric
power generation and recreation, thus water quality management is critical.
Since 2017 the multidisciplinary project ALOP (ALentejo Observation and
Prediction systems) expands the knowledge about the physical and bio-chemical
properties of Alqueva reservoir. This project includes an integrated field
campaign at different experimental sites in the reservoir and its shores, at
least until September 2018. It aims to develop a multi-functional activity in
the field of atmosphere-water-ecosystem interaction, which embraces
observation, prediction and risk alert. It intends to develop tools of
observation, forecasting and alert in the domains of meteorology and water
(quantity and quality), at regional scale. Satellite remote sensing
constitutes a useful tool to complement in situ data sampling and
laboratorial analysis of water quality parameters, which is laborious and
expensive and thus spatially and temporally limited. Unless a water body is
adequately instrumented with in situ sensors, remote-sensing is the only
suitable method to monitor the quality of remote and large inland waters
(WMO, 2013) and can undoubtedly contribute to early warning systems. Several
satellite remote sensing studies have been proposed using a variety of
sensors over a number of worldwide reservoirs (Gholizadeh et al., 2016).
Remote sensing of water bodies<?pagebreak page74?> rely on the varying colour of natural waters
that correspond to different spectral reflectances, assuming that these
variations depend on the water constituents. Water remote sensing was used to
monitor ocean colour already since the 1960s, and in the last three decades
there has been a growing interest to apply these remote sensing techniques
also to inland water quality. For this purpose, remote sensing measurements,
mainly using visible and near-infrared wavelengths, are used to develop
bio-optical models that aim to relate radiometric (optical) and biological
quantities. Inland waters are optically complex due to the presence of
several constituents that may interact, creating uncertainties in the remote
sensing retrievals (Toming et al., 2016; Ogashawara et al., 2017). Thus there
is a need to study inland waters at a local and regional scale and to
quantify the performance of remote sensing methods to monitor inland water
quality. The first remote sensing studies over Portuguese reservoirs were
carried out by the authors, proposing semi-empirical bio-optical models to
estimate concentrations of chlorophyll <inline-formula><mml:math id="M7" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> and cyanobacteria (Potes et al.,
2011), as well as turbidity (Potes et al., 2012) over Alqueva from MERIS
sensor onboard ENVISAT satellite.</p>
      <p id="d1e214">The launch of ESA Sentinel-2 (MSI) mission (S-2A launched in June 2015 and
S-2B launched in March 2017), carrying as single payload the Multi-Spectral
Instrument (MSI), brought a great opportunity to study inland reservoirs. It
presents a systematic global coverage of two to three days at mid-latitudes,
which supports monitoring of changes in reservoirs, with relatively high
spatial resolution. MERIS sensor, on board ENVISAT, presented maximum spatial
resolution of 300 m, whereas MSI presents a spatial resolution of 10, 20 or
60 m, depending on the spectral band. Potes et al. (2011, 2012) proposed a
method to monitor chlorophyll <inline-formula><mml:math id="M8" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>, cyanobacteria and turbidity over inland
reservoirs using MERIS data. The objective of this work is to show the
potential of MSI used with the set of algorithms developed for MERIS, to
study the water quality of inland waters. Specifically, a micro-algae bloom
that occurred in early autumn 2017 is analysed and its evolution related to
the influence of a hurricane progressing over the Eastern North Atlantic
region.</p>
      <p id="d1e224">Section 2 presents the data used and methodology. Results are presented and
discussed in Sect. 3 and finally Sect. 4 summarizes the main conclusions.</p>
</sec>
<sec id="Ch1.S2">
  <title>Data and methods</title>
      <p id="d1e233">Data from Sentinel 2 is used in this work, namely level 2A from MSI
instrument, which corresponds to images with atmospheric correction,
providing information of surface reflectance in 12 spectral channels from 443
to 2190 nm (central wavelength). The product Maximum Chlorophyll Index (MCI)
was also extracted from the level 2 images which is an indicator of the
amount of chlorophyll present in water mass (Gower et al., 2008) and thus a
useful tool in the monitoring of algae blooms of inland waters. The bands
selected for MCI index were the 665, 705 and 740 nm.</p>
      <p id="d1e236">The algorithms from Potes et al. (2011, 2012) developed for MERIS are:

              <disp-formula specific-use="align" content-type="numbered"><mml:math id="M9" display="block"><mml:mtable displaystyle="true"><mml:mlabeledtr id="Ch1.E1"><mml:mtd/><mml:mtd><mml:mstyle class="stylechange" displaystyle="true"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><?xmltex \hack{\hbox\bgroup\fontsize{9.2}{9.2}\selectfont$\displaystyle}?><mml:mi mathvariant="normal">Chl</mml:mi><mml:mspace linebreak="nobreak" width="0.25em"/><mml:mi>a</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">4.23</mml:mn><mml:msup><mml:mfenced open="(" close=")"><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mn mathvariant="normal">560</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow><mml:mrow><mml:mn mathvariant="normal">442.5</mml:mn><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn mathvariant="normal">3.94</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.25em"/><mml:mfenced open="[" close="]"><mml:mrow><mml:mi mathvariant="normal">mg</mml:mi><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfenced><?xmltex \hack{$\egroup}?></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E2"><mml:mtd/><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle displaystyle="true" class="stylechange"/><?xmltex \hack{\hbox\bgroup\fontsize{9.2}{9.2}\selectfont$\displaystyle}?><mml:mi mathvariant="normal">Cya</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">115</mml:mn><mml:mspace linebreak="nobreak" width="0.25em"/><mml:mn mathvariant="normal">530.31</mml:mn><mml:msup><mml:mfenced open="(" close=")"><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mn mathvariant="normal">560</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">nm</mml:mi><mml:mo>⋅</mml:mo><mml:mn mathvariant="normal">620</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow><mml:mrow><mml:mn mathvariant="normal">490</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mn mathvariant="normal">2.38</mml:mn></mml:msup><mml:mspace width="0.25em" linebreak="nobreak"/><mml:mfenced open="[" close="]"><mml:mrow><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mn mathvariant="normal">3</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:mi mathvariant="normal">cells</mml:mi><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">mL</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:mfenced><?xmltex \hack{$\egroup}?></mml:mrow></mml:mtd></mml:mlabeledtr><mml:mlabeledtr id="Ch1.E3"><mml:mtd/><mml:mtd><mml:mstyle displaystyle="true" class="stylechange"/></mml:mtd><mml:mtd><mml:mrow><mml:mstyle class="stylechange" displaystyle="true"/><?xmltex \hack{\hbox\bgroup\fontsize{9.2}{9.2}\selectfont$\displaystyle}?><mml:mi mathvariant="normal">Turb</mml:mi><mml:mo>=</mml:mo><mml:mn mathvariant="normal">8.93</mml:mn><mml:mfenced close=")" open="("><mml:mstyle displaystyle="true"><mml:mfrac style="display"><mml:mrow><mml:mn mathvariant="normal">560</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow><mml:mrow><mml:mn mathvariant="normal">412.5</mml:mn><mml:mspace width="0.125em" linebreak="nobreak"/><mml:mi mathvariant="normal">nm</mml:mi></mml:mrow></mml:mfrac></mml:mstyle></mml:mfenced><mml:mo>-</mml:mo><mml:mn mathvariant="normal">6.39</mml:mn><mml:mspace width="0.25em" linebreak="nobreak"/><mml:mfenced close="]" open="["><mml:mi mathvariant="normal">NTU</mml:mi></mml:mfenced><?xmltex \hack{$\egroup}?></mml:mrow></mml:mtd></mml:mlabeledtr></mml:mtable></mml:math></disp-formula>

          Table 1 presents the information about MERIS bands used in the algorithms to
estimate the concentration of chlorophyll <inline-formula><mml:math id="M10" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> (Chl <inline-formula><mml:math id="M11" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> in Eq. 1), density of
cyanobacteria (Cya in Eq. 2) and water turbidity (Turb in Eq. 3). In the same
table the equivalent MSI wavelengths applied in this work is presented.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1"><caption><p id="d1e413">MERIS bands wavelengths and equivalent MSI bands used in the
algorithms.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="4">
     <oasis:colspec colnum="1" colname="col1" align="right"/>
     <oasis:colspec colnum="2" colname="col2" align="right" colsep="1"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry namest="col1" nameend="col2" align="center" colsep="1">MERIS </oasis:entry>
         <oasis:entry namest="col3" nameend="col4" align="center">MSI </oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">Wavelength</oasis:entry>
         <oasis:entry colname="col2">Bandwidth</oasis:entry>
         <oasis:entry colname="col3">Wavelength</oasis:entry>
         <oasis:entry colname="col4">Bandwidth</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">(nm)</oasis:entry>
         <oasis:entry colname="col2">(nm)</oasis:entry>
         <oasis:entry colname="col3">(nm)</oasis:entry>
         <oasis:entry colname="col4">(nm)</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">412.5</oasis:entry>
         <oasis:entry colname="col2">10</oasis:entry>
         <oasis:entry colname="col3">443</oasis:entry>
         <oasis:entry colname="col4">20</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">442.5</oasis:entry>
         <oasis:entry colname="col2">10</oasis:entry>
         <oasis:entry colname="col3">443</oasis:entry>
         <oasis:entry colname="col4">20</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">490</oasis:entry>
         <oasis:entry colname="col2">10</oasis:entry>
         <oasis:entry colname="col3">490</oasis:entry>
         <oasis:entry colname="col4">65</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">560</oasis:entry>
         <oasis:entry colname="col2">10</oasis:entry>
         <oasis:entry colname="col3">560</oasis:entry>
         <oasis:entry colname="col4">35</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">620</oasis:entry>
         <oasis:entry colname="col2">10</oasis:entry>
         <oasis:entry colname="col3">665</oasis:entry>
         <oasis:entry colname="col4">30</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p id="d1e551">The algorithms represented by Eqs. (1) to (3) were applied now to the same
water body as in Potes et al. (2011, 2012). The chlorophyll <inline-formula><mml:math id="M12" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentration
was also obtained on a bimensal basis from in situ sampling and laboratory
analysis in the framework of ALOP project, in order to validate the results.
The method used was the molecular absorption spectroscopy and the equations
developed by Lorenzen (1967).</p>
</sec>
<sec id="Ch1.S3">
  <title>Study site and case study</title>
      <p id="d1e567">Alqueva reservoir project was concluded in 2002 and the reservoir reached the
capacity of 80 % in March 2004. Figure 1 shows the surface area of the
reservoir at its full capacity as well as the sites considered in this work.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1" specific-use="star"><caption><p id="d1e572">Map of Alqueva reservoir located in Southeast Portugal. The sites
used in this work are also represented.</p></caption>
        <?xmltex \igopts{width=298.753937pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f01.png"/>

      </fig>

      <p id="d1e581">The algorithms developed by Potes et al. (2011, 2012) for MERIS have been
applied to MSI imagery in Alqueva reservoir. ALOP field campaign is ongoing
since January 2017 and a case study of October 2017 was chosen, because this
was a particular month in Portugal with the influence of Ophelia hurricane
amidst a very dry period. Ophelia started as a tropical storm but it reached
category 3 hurricane in Saffir–Simpson hurricane wind scale, South of Azores
islands being the strongest hurricane ever recorded so far East<?pagebreak page75?> in the
Atlantic (Fig. 2). In its trajectory towards Ireland it started to lose
strength as is entered in cold waters being very close to Iberian Peninsula,
about 360 km from Cape Finisterre (Spain).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p id="d1e587">Spinning Enhanced Visible and Infrared Imager (SEVIRI) image of
hurricane Ophelia located South of Azores islands on 14 October 2017, at
18:00 UTC (<uri>https://irishweatheronline.wordpress.com/</uri>, last access:
15 April 2018).</p></caption>
        <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f02.jpg"/>

      </fig>

      <p id="d1e599">This hurricane brought a meteorological breakup window in the unprecedented
drought scenario that the country was facing by October (which is normally
the beginning of the rainy season). In particular, this event led to the
increase of wind speed and relative humidity and a decrease in the air
temperature. Precipitation was concentrated in two days (17 and 18 October)
with an accumulated value of 32.0 mm. Figure 3 shows the evolution of air
temperature for October 2017 recorded in CidAlmeida meteorological station
installed in the area of Alqueva (ALOP project) where the influence of the
hurricane can be detected between 16 and 22 October.</p>
      <p id="d1e602">Figure 4 presents a wind rose from the same inland station for the period 15
to 22 October, where the stronger winds from the South and West quadrants are
clearly visible, as a consequence of hurricane Ophelia passing by Portugal.</p>
      <p id="d1e605">According to this scenario, three Sentinel-2 images from October 2017 were
selected on clear sky days (12, 22 and 29) to use the MSI instrument in
Alqueva reservoir. Table 2 shows acquisitions date and time for both
satellite data and in situ water collection.</p>
</sec>
<sec id="Ch1.S4">
  <title>Results</title>
      <p id="d1e614">On 12 October the reservoir was under a micro-algae bloom especially on the
northern part as can be seen in Fig. 5 (row a) in terms of concentration of
chlorophyll <inline-formula><mml:math id="M13" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>, density of cyanobacteria and water turbidity. Values greater
than 50 mg m<inline-formula><mml:math id="M14" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> of chlorophyll <inline-formula><mml:math id="M15" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> were estimated for the northern
part, as well as greater than 75 000 cells mL<inline-formula><mml:math id="M16" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> cyanobacteria with
turbidity values reaching 30 NTU.</p>
      <p id="d1e655">On 22 October (Fig. 5 – row b), six days after, all the three parameters
decreased sharply in the northern part probably due to very different weather
conditions in the six days under the influence of the hurricane Ophelia
passage along<?pagebreak page76?> the Portuguese coast. It is well known that lower temperatures
inhibit the phytoplankton growth (Wu et al., 2015) the same occurs with
increasing wind speed and precipitation, which leads to increasing in water
mixing (Fleming-Lehtinen and Laamanen, 2012). For these reasons a regress of
the bloom due to the changes in meteorological conditions was expected.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2"><caption><p id="d1e661">MSI acquisition dates and in situ date for water collection.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="3">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1">Date</oasis:entry>
         <oasis:entry colname="col2">Time (UTC)</oasis:entry>
         <oasis:entry colname="col3">Type</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">12 Oct 2017</oasis:entry>
         <oasis:entry colname="col2">11:21</oasis:entry>
         <oasis:entry colname="col3">Satellite</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">22 Oct 2017</oasis:entry>
         <oasis:entry colname="col2">11:21</oasis:entry>
         <oasis:entry colname="col3">Satellite</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">27 Oct 2017</oasis:entry>
         <oasis:entry colname="col2">11:00–14:00</oasis:entry>
         <oasis:entry colname="col3">Laboratory</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">29 Oct 2017</oasis:entry>
         <oasis:entry colname="col2">11:12</oasis:entry>
         <oasis:entry colname="col3">Satellite</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p id="d1e741">In the central part of the reservoir the values are above the eutrophic
threshold for chlorophyll <inline-formula><mml:math id="M17" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> presented by Bukata et al. (1995), of
6 mg m<inline-formula><mml:math id="M18" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. In addition, most of the branches of reservoir present
values are above the ecological potential and eutrophic threshold for
chlorophyll <inline-formula><mml:math id="M19" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> for reservoirs in the South of Portugal, which according with
the Water Frame Directive is 9.5 and 8 mg m<inline-formula><mml:math id="M20" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>, respectively (INAG,
2009). Nine days after 22 October, on the images of 29 October presented in
Fig. 5 (row c) the reservoir is clear from the presence of the micro-algae
bloom. All the three parameters present low values indicating good water
quality on that day. Nevertheless, some thinner branches of the reservoir
still present some occasional high values. A summary table with minimum,
maximum and mean values is presented for the three parameters in the three
days (Table 3).</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p id="d1e785">One-minute averages of air temperature recorded in CidAlmeida
meteorological station located inland nearby Alqueva-Montante site (Fig. 1)
for October 2017.</p></caption>
        <?xmltex \igopts{width=241.848425pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f03.png"/>

      </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p id="d1e796">Wind rose recorded in a meteorological station located inland nearby
Alqueva-Montante site (Fig. 1) for the period 15 to 22 October 2017.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f04.png"/>

      </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F5" specific-use="star"><caption><p id="d1e807">Concentration of chlorophyll <inline-formula><mml:math id="M21" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>, density of cyanobacteria and water
turbidity estimated from the Eqs. (1) to (3) for 12 October (row <bold>a</bold>),
22 October (row <bold>b</bold>) and 29 October (row <bold>c</bold>).</p></caption>
        <?xmltex \igopts{width=341.433071pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f05.jpg"/>

      </fig>

      <p id="d1e832">Figure 6 presents a scatter plot between the MCI and concentration of
chlorophyll <inline-formula><mml:math id="M22" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> obtained from satellite. All pixels from 22 October are used
in the plot, in a total of 28 251 points. These two parameters are well
correlated (correlation coefficient of 0.70) with a RMSE (Root Mean Square
Error) of 21.5 mg m<inline-formula><mml:math id="M23" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. Future work foresees the use of longer data
series to quantify MCI as chlorophyll concentration.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6"><caption><p id="d1e857">Scatter plot between MCI and concentration of chlorophyll <inline-formula><mml:math id="M24" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> estimated
by Eq. (1) for day 22 October all pixels.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f06.png"/>

      </fig>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><caption><p id="d1e876">Range and mean values of the maps presented in Fig. 5.</p></caption><oasis:table frame="topbot"><?xmltex \begin{scaleboxenv}{.90}[.90]?><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row>
         <oasis:entry colname="col1">Date</oasis:entry>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3">Chlorophyll <inline-formula><mml:math id="M25" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula></oasis:entry>
         <oasis:entry colname="col4">Cyanobacteria</oasis:entry>
         <oasis:entry colname="col5">Turbidity</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2"/>
         <oasis:entry colname="col3">[mg m<inline-formula><mml:math id="M26" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>]</oasis:entry>
         <oasis:entry colname="col4">[10<inline-formula><mml:math id="M27" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">3</mml:mn></mml:msup></mml:math></inline-formula> cells mL<inline-formula><mml:math id="M28" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>]</oasis:entry>
         <oasis:entry colname="col5">[NTU]</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>
         <oasis:entry colname="col1">12 Oct</oasis:entry>
         <oasis:entry colname="col2">Range</oasis:entry>
         <oasis:entry colname="col3">[2.6; 600.1]</oasis:entry>
         <oasis:entry colname="col4">[0.1; 228.1]</oasis:entry>
         <oasis:entry colname="col5">[1.5; 25.0]</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">Mean</oasis:entry>
         <oasis:entry colname="col3">46.1</oasis:entry>
         <oasis:entry colname="col4">33.3</oasis:entry>
         <oasis:entry colname="col5">8.6</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">22 Oct</oasis:entry>
         <oasis:entry colname="col2">Range</oasis:entry>
         <oasis:entry colname="col3">[0.5; 263.7]</oasis:entry>
         <oasis:entry colname="col4">[0.2; 283.0]</oasis:entry>
         <oasis:entry colname="col5">[0.1; 19.1]</oasis:entry>
       </oasis:row>
       <oasis:row rowsep="1">
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">Mean</oasis:entry>
         <oasis:entry colname="col3">14.1</oasis:entry>
         <oasis:entry colname="col4">4.0</oasis:entry>
         <oasis:entry colname="col5">4.5</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1">29 Oct</oasis:entry>
         <oasis:entry colname="col2">Range</oasis:entry>
         <oasis:entry colname="col3">[0.1; 140.1]</oasis:entry>
         <oasis:entry colname="col4">[0.1; 179.7]</oasis:entry>
         <oasis:entry colname="col5">[0.3; 15.3]</oasis:entry>
       </oasis:row>
       <oasis:row>
         <oasis:entry colname="col1"/>
         <oasis:entry colname="col2">Mean</oasis:entry>
         <oasis:entry colname="col3">4.6</oasis:entry>
         <oasis:entry colname="col4">3.8</oasis:entry>
         <oasis:entry colname="col5">1.2</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup><?xmltex \end{scaleboxenv}?></oasis:table></table-wrap>

      <p id="d1e1079">Satellite derived results were compared with data obtained from laboratory
analysis. Unfortunately, there are no water laboratory analyses for the same
days as MSI acquired images, rather five days before (22 October) and two
days after (29 October). From the analysis of MSI retrieved data, it was
concluded that the water quality has improved from 22 to 29 October and thus
it is expected that the water analysis should be more or less similar or
in-between the values of MSI. This is shown in Fig. 7 where the
chlorophyll <inline-formula><mml:math id="M29" display="inline"><mml:mi>a<?pagebreak page77?></mml:mi></mml:math></inline-formula> concentration estimated from MSI (22 and 29 October) and
obtained in laboratory (27 October) for five sites (Fig. 1) is plotted.
The results are generally in agreement. From 22 to 29 October, MSI reports a
decrease in chlorophyll <inline-formula><mml:math id="M30" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> concentration and the laboratory analysis (middle
day) confirms this decrease presenting a middle value in all sites, except
for Alqueva-Montante and Site 1, which presents a very similar value
nevertheless slightly greater than the MSI value for 22 October. In these
two sites the MSI values, nearby the in situ measurement place, were more
heterogeneous than in the other sites probably due to their central location
where the water is under more currents than in the other sites, in this part
of the year. The results also suggest that the decrease of chlorophyll <inline-formula><mml:math id="M31" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> was
not linear in time, but more pronounced near the end of the five day period.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7"><caption><p id="d1e1105">Bar plot of concentration of chlorophyll <inline-formula><mml:math id="M32" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula> estimated by Eq. (1)
for 22 and 29 October and obtained in laboratory for 27 October for 5 sites shown on Fig. 1.</p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://piahs.copernicus.org/articles/380/73/2018/piahs-380-73-2018-f07.png"/>

      </fig>

</sec>
<?pagebreak page78?><sec id="Ch1.S5" sec-type="conclusions">
  <title>Conclusions</title>
      <p id="d1e1128">In this work the potential of Sentinel-2 MSI instrument for monitoring the
water quality of inland waters is shown. In the case study reported,
different conditions of Alqueva reservoir are analysed for one month. Systems
like Alqueva reservoir are highly dynamic and respond rapidly to changes in
atmospheric conditions, thus is very importance to have these kinds of tools
for monitoring the water surface as a whole. In this work, a set of
algorithms developed for another space borne spectroradiometer (MERIS) were
applied with good results. The team is now working to tune the algorithms in
order to make use of the full potential of MSI instrument. Specific
algorithms were already developed successfully by Toming et al. (2016) using
the same MSI instrument over Estonian lakes, regarding chlorophyll <inline-formula><mml:math id="M33" display="inline"><mml:mi>a</mml:mi></mml:math></inline-formula>
concentration as well as colored dissolved organic matter (CDOM) and
dissolved organic carbon (DOC).</p>
</sec>

      
      </body>
    <back><notes notes-type="dataavailability">

      <p id="d1e1142">Data used in this work is available on request to the first
author.</p>
  </notes><notes notes-type="authorcontribution">

      <p id="d1e1148">MP conceptualized and led the team
on this research. He also wrote great part of the manuscript and carried out
the corrections during the write-up. GR gathered, processed and prepared the
spatial data and maps used for this article. AMP and MHN were responsible for
the in situ and laboratory data analysis used in the work. MJC participated
in the data processing and discussion and wrote the first part of the
manuscript. RS and MMM participated in the discussion of results and reviewed
the manuscript for necessary corrections.</p>
  </notes><notes notes-type="competinginterests">

      <p id="d1e1154">The authors declare that they have no conflict of
interest.</p>
  </notes><notes notes-type="sistatement">

      <p id="d1e1160">This article is part of the special issue “Earth Observation
for Integrated Water and Basin Management: New possibilities and challenges
for adaptation to a changing environment”. It is a result of The Remote
Sensing &amp; Hydrology Symposium, Cordoba, Spain, 8–10 May 2018.</p>
  </notes><ack><title>Acknowledgements</title><p id="d1e1166">The work was funded by the ALOP project (ALT20-03-0145-FEDER-000004) and also
through the European Union through the European Regional Development Fund,
included in the COMPETE 2020 (Operational Program Competitiveness and
Internationalization) through the ICT project (UID/GEO/04683/2013) with the
reference POCI-01-0145-FEDER 007690.<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?> Edited
by: María José Polo<?xmltex \hack{\newline}?> Reviewed by: two anonymous
referees</p></ack><ref-list>
    <title>References</title>

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  </ref-list></back>
    <!--<article-title-html>Use of Sentinel 2 – MSI for water quality monitoring at Alqueva reservoir, Portugal</article-title-html>
<abstract-html><p>Alqueva reservoir located in southeast of Portugal has a surface area of
250&thinsp;km<sup>2</sup> and total capacity of 4150&thinsp;hm<sup>3</sup>. Since 2006 the water
quality of this reservoir is explored by the authors using remote sensing
techniques. First using MERIS multi-spectral radiometer on-board of ENVISAT-1
and presently with MSI multi-spectral radiometer on-board SENTINEL-2. The
existence of two satellites (A and B) equipped with MSI enable the area to be
revisited, under the same viewing conditions, every 2–3 days. Since 2017 the
multidisciplinary project ALOP (ALentejo Observation and Prediction systems)
expands the team knowledge about the physical and bio-chemical properties of
the reservoir. This project includes an integrated field campaign at
different experimental sites in the reservoir and its shores, at least until
September 2018. Previous algorithms developed by the team for MERIS are
tested with the new MSI instrument for water turbidity, chlorophyll <i>a</i>
concentration and density of cyanobacteria. Results from micro-algae bloom
occurred in late summer/early autumn 2017 on the reservoir are presented,
showing the capabilities of MSI sensor for detection and high resolution
mapping over the reservoir. The results are compared with in situ sampling
and laboratorial analysis of chlorophyll <i>a</i> associated with the bloom.</p></abstract-html>
<ref-html id="bib1.bib1"><label>1</label><mixed-citation>
Bukata, R. P., Jerome, J. H., Kondratyev, K. Y., and Pozdnyakov, D. V.:
Optical Properties and Remote Sensing of Inland and Coastal Waters, 135–250,
CRS Press, Boca Raton, Florida 33431, USA, 1995.
</mixed-citation></ref-html>
<ref-html id="bib1.bib2"><label>2</label><mixed-citation>
Fleming-Lehtinen, V. and Laamanen, M.: Long-term changes in Secchi depth and
the role of phytoplankton in explaning light attenuation in the Baltic Sea,
Estuar. Coast. Shelf S., 102–103, 1–10, 2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib3"><label>3</label><mixed-citation>
Gholizadeh, M. H., Melesse, A. M., and Reddi, L.: A Comprehensive Review on
Water Quality Parameters Estimation Using Remote Sensing Techniques, Sensors,
16, 1298, <a href="https://doi.org/10.3390/s16081298" target="_blank">https://doi.org/10.3390/s16081298</a>, 2016.
</mixed-citation></ref-html>
<ref-html id="bib1.bib4"><label>4</label><mixed-citation>
Gower, J. F., King, R. S., and Goncalves, P.: Global monitoring of plankton
blooms using MERIS MCI, Int. J. Remote Sens., 29, 6209–6216,
<a href="https://doi.org/10.1080/01431160802178110" target="_blank">https://doi.org/10.1080/01431160802178110</a>, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib5"><label>5</label><mixed-citation>
INAG (Instituto da Água Instituto Público): Critérios para a
Classificação do Estado das Massas de Água Superficiais – Rios e
Albufeiras, Ministério do Ambiente, do Ordenamento do Território e do
Desenvolvimento Regional, Lisboa, Portugal, 2009.
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