The Global Surface Water Explorer (GSWE) was combined with bathymetric and historical meteorological data to quantify water balance during the period 1984–2020 in the Primera de Palos freshwater lagoon (Southwest Spain). The results showed that the natural hydrological regime of the lagoon was modified from 1995 by water inputs from irrigation returns. Thanks to a water balance approach, these irrigation returns were quantified as the closure term of the water balance.