The northern end of Lake George, Uganda, and its associated wetlands receive localized metal pollution from a former copper mine and tailings left after metal extraction. The aim of this study was to determine (i) whether the heavy metals are a threat to the biology of the major commercial fish species and (ii) whether consumption of the fish threatens human health. Concentrations of copper, zinc, cobalt and nickel in detrital sediments, plankton, and five fish species from sites in Lake George, the Kazinga Channel and Lake Edward (which are inter-connected) were determined using atomic absorption spectroscopy. The detrital sediments of Hamukungu Bay, Lake George, had average concentrations (μg/g dry weight) of 96.3 zinc, 270.4 copper, 57.4 cobalt and 42.8 nickel. There were no significant differences between the Hamukungu Bay and the North Lake George site of Bushatu: both receive inflows from the mining activities. Concentrations of copper and zinc were significantly higher than background values from unpolluted freshwater ecosystems. Plankton samples showed a metal concentration gradient consistent with a gradient from the source of pollution in northern Lake George, along the Kazinga Channel to Lake Edward. The liver tissues of fish had markedly higher concentrations of copper and zinc than flesh. Concentrations of cobalt and nickel were relatively low. The highest mean concentrations of metals in liver tissue occurred in Oreochromis leucostictus (189.0 μg/g Cu) and Bagrus docmac (187.5 μg/g Zn) whilst the lowest occurred in Oreochromis niloticus (15.3 μg/g and 78.2 μg/g dry weight copper and zinc, respectively). However, O. niloticus contained the highest concentrations of cobalt (11.2 μg/g) and nickel (3.8 μg/g). Liver Somatic Indices (LSI) of the fish species from the different sites indicated a reduction of LSI in those fish from the most contaminated zones of northern Lake George compared with all other sites. This suggests there could be anatomical and physiological abnormalities linked to the heavy metal pollution. The flesh had only low concentrations of metals; well within international guidelines for consumption. A person would have to consume 9 kg of fresh flesh of Clarias sp. and 65 kg of O. leucostictus daily to exceed the WHO recommended intake for copper, and even more for other metals. This implies that currently metal pollution in Lake George presents an ecological rather than a human health concern.