Cage aquaculture in tropical lakes is an efficient means of generating fish protein to ensure food security and support livelihoods. However, it has been repeatedly criticized as injurious to lake ecosystems due to eutrophication and other problems, and therefore ill-advised. This study examined the impacts of Nile tilapia (Oreochromis niloticus) cage farming on water quality across spatial scales in the world’s largest tropical lake, Lake Victoria. The primary objectives were to determine if water quality patterns differed between cage and control stations along a background limnological gradient, and to identify the water quality variables that contributed most to these differences. We postulated that the spatial arrangement of sites in the lake would drive overarching patterns of water quality variation, while cage aquaculture would have additional impacts on these parameters across the spatial gradient. Water column samples were collected from both cage and control stations at four locations along a known gradient in limnology, across 2 years. The results revealed significant differences in water quality between cage and control stations at all four sites, with dissolved oxygen, pH, and silica contributing the most to these differences. These findings highlight the need for site-specific management strategies to both mitigate the environmental impacts of cage aquaculture in tropical lakes and ensure continuity of aquaculture production. Our study provides an approach that can be applied to tropical lakes and reservoirs around the world. Effective nutrient management and continuous monitoring are recommended to support sustainable aquaculture in ecosystems under stress from growing lakeside populations.