This study evaluates the levels of natural radioactivity in sediment and water samples from Lake Victoria in Jinja, Uganda, with a focus on the radionuclides potassium-40 (40 K), radium-226 (226Ra), and thorium-232 (232Th). We investigated four distinct zones around the lake: fishing (Zone A), farming (Zone B), domestic/livestock (Zone C), and a control zone (Zone D). A total of 15 sediment samples and 15 water samples were collected and analyzed. Sediment samples were obtained using a gravity corer, with a maximum penetration depth of 50 cm. 40 K ranged from 170.479 to 524.883 Bqkg−1 across all zones, 226Ra ranges from 1.51 to 56.78 Bqkg−1 across all zones, and 232Th ranges from 18.18 to 73.10 Bqkg−1 across all zones. 40 K concentrations were highest in the farming zone, likely due to the use of nitrogen, phosphorus, and potassium (NPK) fertilizers. 226Ra and 232Th levels were also elevated in the farming zone, suggesting potential contributions from phosphate fertilizers. Absorbed dose rates varied across the zones, ranging from 28.33 to 58.17 nGyh-1. The measured absorbed dose rates across all zones were within the global average of 59 nGyh−1. The effective annual dose rate ranged from 0.35 to 0.91 mSvy−1 across all zones. Effective annual dose rates did not exceed the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) recommended limit of 1 mSv y−1, indicating low risks to public health from sediment radioactivity. The external index was below the safety threshold, suggesting minimal health risks. In water samples, gross alpha and beta activity concentrations were analyzed. Zone B had the highest average alpha activity concentration (0.64 BqL−1) and beta activity concentration (0.72 BqL−1), while Zone A had the lowest for both alpha (0.16 BqL−1) and beta (0.25 BqL−1) activity concentrations. Gross beta activity was generally higher than gross alpha activity, reflecting potential anthropogenic influences. Most water samples were within the UNSCEAR recommended limits for drinking water quality, except in areas affected by agricultural runoff. This study demonstrates that while the sediments of Lake Victoria in Jinja, Uganda, exhibit varying levels of naturally occurring radionuclides influenced by farming practices, the overall radiation exposure remains within safe limits. Continuous monitoring and regulatory measures are essential to maintain these safety levels and mitigate potential risks from increasing agricultural activities.