Lakes in arid regions are ecologically valuable yet highly fragile due to intense evaporation. To provide an extra water supply for maintaining water balance in lakes, the Ecological Replenishment Water Program (ERWP) in northwest China has significantly changed the hydrological and hydrochemical conditions for these lakes. Descriptive statistics and water and mass balances, together with hydrogeochemical modeling were used in this study to gain an understanding of the impacts of water replenishment (irrigation and drainage water) on evolution for Shahu Lake. A virtual sample was introduced in NETPATH hydrogeochemical modeling to compute the net chemical reactions in the lake water. Variations in TDS indicated that the lake evolved to be saline during 2004–2012 (stage I) and then tended to be fresh during 2013–2014 (stage II). Results highlighted that groundwater outflow and chemical reactions were the overriding factors controlling chemical evolution in the lake system, which greatly depend on the replenishment activities. The salinity reduction from the virtual samples to the final samples were attributed to the precipitation of calcite and dolomite, dissolution of gypsum, Na-K and Na-Ca exchange, and the CO2 degassing in the lake system at an annual scale of 0.11 g/L in stage I and 0.15 g/L in stage II. The quality of replenishment water was as important as quantity for rehabilitating lakes, as it significantly determines the occurrence of chemical reactions in lake water. Findings from this paper can provide insight into the evolution of arid lakes in response to replenishment activities and can help contribute to better management of a valuable and fragile resource.