The salinization of freshwater lakes by agricultural activities poses a threat to many lake ecosystems around the world. Quantitative, medium- to long-term studies are needed to understand how some common agricultural practices, such as the discharge of crop irrigation in the vicinities of large lakes, may affect lake salinization. In this study, hydrological, hydrodynamics, water quality and meteorological datasets were used to analyze the long-term spatial-temporal variations of water salinities of a major lake, the Chagan Lake, in Northeast China. An integrated hydrodynamics-salinity model was used to simulate lake water salinity changes taking place at different times and locations, including (i) salt accumulations during a non-frozen period, and (ii) the time when water salinity may reach a significant threshold (1 psu) that jeopardizes a major environmental and economic value of this lake (i.e., the cultivation of local fish species). The results confirmed that Chagan Lake was indeed undergoing salinization in the ten year period between 2008 and 2018. The spatial-temporal patterns of the salinization processes were identified. For instance, (i) the mean salinity of the lake water was found to be 0.55 psu in the summer season of the region and 0.53 psu in the winter, and (ii) between May to October the salinity was up to 0.62 psu in the western region of the lake. The rate of salt accumulation was found to be 97 ton per annum during the non-frozen period. The simulation predicted that by 2024 the lake water will become sub-saline (salinity > 1.07 psu) which is toxic to fish species, if the current practice of irrigation discharge into the lake continues. In the scenario that the amount of irrigation discharges into the lake doubles, the western region of the lake will become sub-saline within one year, and then the whole lake within three years. Overall, this study has produced results that are useful to authorities around the world, for balancing the risks and benefits of developing crop irrigation fields in areas surrounding large freshwater lakes.