As the largest freshwater lake in China, water environmental pollution in Poyang Lake is increasingly attracting attention. However, to date, the occurrence of seldom-monitored trace elements (SMTEs) (such as thallium (Tl) and cobalt (Co)) and their potential ecological influences in the Poyang Lake area remain unclear. Here, geochemical baseline concentrations (GBCs) were employed to investigate anthropogenic inputs of these two metals (Tl and Co) and were used to assess the potential ecological risk in surface sediments of Poyang Lake. The results showed that the mean concentrations of Tl and Co were 1.11 mg/kg and 15.42 mg/kg, respectively, slightly higher than background values (BVs) in local soil. Spatially, the Co concentrations in surface sediments of Poyang Lake varied; Co concentrations in the west of the study area were significantly lower than in the middle of the lake. In contrast, no significant spatial variation of Tl was found in studied areas of Poyang Lake. Average GBCs were similar to the mean measured concentrations of Tl and Co in the lake, and both were higher than the BVs in local soil. In anthropogenic source analysis based on the GBCs, 47.22% samples and 41.67% samples were influenced by human activity for Tl and Co, respectively; the mean anthropogenic contribution rate was 5.90% for Tl (0.43 to 16.22%), and 13.01% for Co (0.82 to 31.59%). These results indicated that Tl and Co mainly originate from natural processes. However, the anthropogenic contribution should not be ignored. Moreover, the geo-accumulation index (Igeo) and potential ecological parameter (Er) generally indicated no contamination and a low potential risk for Tl and Co in Poyang Lake sediments, which used the GBCs as BVs. The results of this study suggest that GBCs are more scientifically robust and practical as a reference than BVs. They can also be used when BVs are lacking.