Water balance is considered as an important tool to assess the amount of water and its availability in a region. The Small Aral Sea is a salt lake in the territory of the Kyzylorda region of Kazakhstan, the Northern part of the shrinking Aral Sea, receiving water from the Syr Darya, as a result of lowering of the water horizon of the Aral Sea and with the onset of 40–40.2 m in 1987, when the Berg Strait was formed. In this study, water balance assessment in the Small Aral Sea has been done from 1987 to 2014. The water balance of the Small Aral Sea during the observation period is mainly determined by river runoff, precipitation and evaporation. The general tendency of precipitation decreased slightly, while the general tendency for evaporation increase is high. The annual inflow of the river into the Small Aral Sea increased from 1 km3 in 1987 to 5 km3 in 2014 while its water balance increased from − 1.4 to 2.44 km3. As the result, the water volume of the Small Aral Sea increased by 6% and the water surface area by 4% during the analyzed period.