Lake water salinization in arid areas is a common problem and should be controlled for the better use of freshwater of lakes and for the protection of the environment around lakes. It is well known that the increasing of hydraulic connectivity improves water quality, but for a lake, understanding how hydraulic connectivity changes its water quality in terms of spatial aspects is of great significance for the protection and utilization of different regions of the lake water body. In this paper, the impacts of three connectivity scenarios on the spatial-temporal salinity changes in Bosten Lake were modeled through the three-dimensional (3D) hydrodynamic model, Environmental Fluid Dynamics Code (EFDC). The constructed Bosten Lake EFDC model was calibrated for water level, temperature, and salinity with acceptable results. As for the Bosten Lake, three connectivity scenarios were selected: (1) the increasing of the discharge water amount into the lake from the Kaidu River, (2) the transferring of 1 million cubic meter freshwater to the southwestern part of the lake (the Huangshuigou region of the lake), and (3) the changing of the outflow position from the southwestern part of the lake (the Kongque river) to the southeastern of the lake (the Caohu region). Through the simulations, we found that the region of the lake mainly influenced by the three scenarios presented here were different, and of the three scenarios, scenario 3 was the best means of controlling the overall lake salinity. On the basis of the salinity distribution results gained from the simulations, decision-makers can choose the ways to mitigate the salinity of the lake according to which region they want to improve the most in terms of economic efficiency and preserve in terms of ecological balance.It is a common problem that water is salinized with time in arid and semi-arid areas [5,6]. In Central Asia, many freshwater lakes have changed to oligosaline or saline lakes due to anthropogenic activities and climate change [7]. Lake Qarun, southwest of Cairo, Egypt, a formerly freshwater lake, has become a saline lake due to agricultural drainage [8]. The water salinity of the Aral Sea and Lake Chad has increased due to river regulation and diversions [9]. In arid and semi-arid regions, lake water salinization has been attributed primarily to high water evaporation rates, low rainfall rates, limited recharge and inflow water diversion for irrigation, among other uses [10][11][12].The impacts of water salinization are manifold, adverse, and have largely irreversible environmental, economic, and social costs [8]. Many studies [13][14][15][16][17] demonstrate that the high salinity in lake water has harmful effects on water quality and the health of people, plants, and animals, hence restricting the utilization of water and damaging the integrity of ecosystems.It is well known that water connectivity is important for controlling water quality and improving ecological environment. The river loop connection, existing prior to 1965, between the Keelung River a...