Temperature-conductivity diagrams are shown as a valid instrument to analyze the hydrographic structure of freshwater ecosystems, even along the surface waters. We put this method in practice in the Ugandan inshore waters of Lake Victoria. A complementary parameter (T-C anomaly) was used to differentiate between upland water intrusions. The relative value of the T-C anomaly provided information about the nature of the water intrusions and showed a considerable correlation with the biological characteristics of the water masses. The results indicated that the connections between catchment attributes, water characteristics, and biological community are quite direct in the inshore waters of Lake Victoria.