Water purification capacity (WPC), a crucial regulator of aquatic ecosystem services, plays an important role in mitigating non-point source pollution and ensuring water quality in a basin. In this study, the long-term water purification capacity of the three countries surrounding Lake Victoria (Kenya, Tanzania and Uganda) was investigated using multi-source remote sensing data. and furthermore, the relationship between water purification and phytoplankton blooms, as well as anthropogenic activities, was exlored. By applying InVEST model, nitrogen and phosphorus (N/P) retention and output were derived, which were utilized to quantitatively assess reginal WPC. High resolution, long-term (2000–2021) spatial distribution of water purification capacity index (WPI) were then generated. The results reveal significant spatiotemporal changes of WPI, with a general trend of initial decline followed by subsequent increase being observed. Notably, comparatively lower WPI was exhibited by Uganda than by Tanzania and Kenya. Among the anthropogenic factors, the frequency of phytoplankton blooms was identified as serving as a spatial validation of WPI. While a significant negative correlation between WPI and GDP was demonstrated, its correlation with population was found to be considerably weaker. These findings contribute significantly to transboundary water resources management and sustainable development, and provide information support for the maintenance of regional ecological health.