The enrichment of bottom sediments with trace elements due to anthropogenic factors is of growing concern worldwide. With the development of industry, agriculture, and urbanization, the risk of freshwater contamination with trace elements is increasing. As trace elements are poorly soluble in water, they have a tendency to accumulate in bottom sediments. The study focused on the evaluation of the trace element contents in the surface layer of bottom sediments of Lake Raczyńskie, located in Poland, and assessing the risks posed by these sediments. The pollution of bottom sediments was estimated based on the index of the geo-accumulation (Igeo), enrichment factor (EF), Nemerow multi-factor index (Pn), and pollution load index (PLI). The assessment of environmental risk was evaluated by the potential ecological risk index (RI) and mean PEL quotient method. The results obtained showed that the average contents of Cd, Cu, Ni, Pb, and Zn exceeded the national geochemical background values (Bn), indicating possible enrichment of bottom sediments due to human activity. Only for Mn were the observed contents below the Bn. This evaluation was confirmed by the PLI and Pn values, which indicated sediment pollution from anthropogenic sources. However, the risk assessment by RI and mean PEL showed a low risk of contamination. The results of principal component analysis (PCA) and values of Igeo and EF suggested that Cd, Cu, Mn, and Zn mainly originate from geogenic sources, while Ni and Pb probably come from an unrecognized anthropogenic source. The distribution of Cd, Mn, and Ni depended on the contents of silt and clay fractions. Additionally, organic carbon influenced Cu, Mn, Ni, and Zn contents in bottom sediments.