A study of trace metal (TM) contamination was conducted at Lake Tonga (Algeria), a site surrounded by several indirect contamination point sources such as an abandoned mine and steelworks. Studying two sampling sites over four seasons, we were able to depict the spatial and temporal variability of TM contamination in the lake. Among the seven TM examined (Pb, Cd, Fe, Zn, Ni, Cu, and Cr), only Fe, Pb, and Cd showed concentrations significantly higher than the site's geological background. The contamination index (sediment concentration/background concentration) calculated for these three TM (Cd = 1.9 ± 1.6, Fe = 6.8 ± 1.8, and Pb = 3.3 ± 2.6) clearly indicated anthropogenic contamination. Sediment TM contamination differed both between sampling sites and seasons despite environmental variables (e.g., oxygen and pH) being similar, thus suggesting different TM contamination sources. Fe contamination was high at the two sampling sites and over all studied seasons, possibly indicating general lake-scale Fe contamination, probably related to atmospheric deposition of steelworks emissions both on the lake and within the watershed. Lake tributaries were further suspected of channeling Fe contamination from the watershed into the lake. On the other hand, the sampling site close to the outlet was especially rich in Cd and Pb typically reflecting contamination by mine wastes. The indirect connection between the abandoned mine and the lake indicates that runoff of mine leachates through groundwater was likely a candidate in explaining the specificity of the TM contamination in this part of the lake. This study provides insights for management of TM contamination by addressing both spatial and temporal variability within the lake as well as differences in contamination sources.