Presented paper is our first step in developing a geoscientific stack of models for an assessment of the Small Aral Sea basin current hydrological conditions within the interdisciplinary SMASHI project (smashiproject.github.io). Based on coupling state-of-the-art physically-based hydrological and machine learning models we have developed the skillful model for the Syr Darya river runoff prediction. This result is the key to understanding water balance trends in vulnerable Aral Sea region.