Non-point source pollution is an important source of ecological risk in karst lakes. The process of source–sink landscapes is the main pathway of pollution migration and plays an important role in water quality. In this study, the ecological risk evolution in the past 30 years was studied in a karst lake watershed with 495 sub-basins as the basic evaluation unit, and the risk assessment model of non-point source pollution was improved by using rainfall and fertilizer application. The results show that (1) the area of cultivated land shrank significantly, with forest land and construction land showing an upward trend in general; (2) the layout of the sink landscape continuously shrank, while the source landscape gradually expanded, and the space of high load values further increased and shifted from a flower-like layout distribution to concentrated contiguity, with some values exceeding 0.5; (3) the 252 sub-watersheds of the sink landscape migrated from very low risk to low risk, while the risk of the source landscape changed from medium risk to high and very high risk in 48 sub-watersheds; and (4) in terms of the overall trend of ecological risk transformation of the source–sink landscape, the transformation of sink landscapes to source landscapes was greater than that of source landscapes to sink landscapes, and the overall ecological risk showed an increasing trend.