The concentrations, sources, and risks of heavy metals (Fe, Al, Mn, Cr, Co, Ni, Cu, Zn, As, Cd, W, Pb, and Tl) in sediments in five river-lake ecosystems in the Poyang Lake region were studied. The concentrations of the heavy metals varied spatially, with most of the highest concentrations in the Raohe river-lake ecosystem (RH). All heavy metals except As, Cd, W, and Tl were enriched in sediments possessing high total organic carbon contents or in finer sediments. Based on enrichment factors and statistical methods, it was found that Cd in sediments in the Xiushui (XS), Ganjiang (GJ), Xinjiang (XJ) river-lake ecosystems, and RH; Mn in the XS, GJ, and RH; and W in the XS and GJ were greatly affected by anthropogenic inputs. Moreover, the origins of Cu, Zn, and As require more attention due to the high concentrations found. The high enrichment factor of Cd in the sediments indicated that this metal might cause significant pollution in the environment. The results of the modified potential ecological risk index revealed that the XS, GJ, RH, and XJ were at considerable ecological risk, while the sediments in the Fuhe river-lake ecosystem (FH) were at moderate ecological risk, with Cd contributing the highest proportion of risk. The hazard score fundamentally validated the modified potential ecological risk analysis and revealed a mean toxicity of 57.80% to the benthic organisms in the RH.