Heavy metals play a crucial role in the environment due to their toxicity, persistence, and bioaccumulation ability, which can lead to severe ecological and health risks. This study aimed to investigate the impact of urbanization and agricultural practices on the heavy metal content in the sediments of the Bug River catchment. To this end, 96 surface sediment samples were collected from various points in the Bug River catchment, including from urban, agricultural, and forested areas. The samples for laboratory analysis were collected in July 2018, 2019, and 2020 in the Polish part of the Bug River watershed. Heavy metal (Zn, Pb, Cr, Ni, Cu, Fe, Mn, and Cd) concentrations were determined using atomic absorption spectroscopy (AAS). The geoaccumulation index (Igeo), contamination factor (CF), and pollution load index (PLI) were used to assess the degree of sediment contamination. The results indicate higher concentrations of heavy metals in urban sediments, where cadmium concentrations reached up to 2.5 mg/kg, compared to agricultural and forested areas, where concentrations were significantly lower. The average Igeo value for cadmium was 0.24 in agricultural areas and 0.15 in urban areas, suggesting the predominance of anthropogenic influences over natural sources. The highest PLI values were found in urban areas, reaching a maximum of 0.33, indicating higher pollution levels. Statistical analysis revealed that urban emissions and agricultural activities significantly influenced the presence of these metals in the Bug River sediments. This study’s conclusions emphasize that effective river water quality management requires continuous monitoring and an understanding of anthropogenic and natural pollution sources. The results contribute to a better understanding the interactions between human activities and water quality, crucial for planning protection and remediation strategies. Additionally, this study provides critical insights into optimizing pollution management strategies and developing remediation methods, serving local and regional policymakers in planning protective actions.