Heavy metals (HMs) in sediment samples (Dry and Rainy seasons) of industrially affected rivers were quantified by Energy Disperse X-ray Fluorescence in the Shitalakshya river of Bangladesh. This study assesses the potential health concerns provided by various HMs manganese (Mn), zinc (Zn), copper (Cu), arsenic (As), lead (Pb), cadmium (Cd), nickel (Ni), and chromium (Cr). Mean concentration of HMs ranked as Mn > Zn > Cu > Cr > Ni > Pb > As > Cd for both seasons, where almost all the elements were found within the standard limit, except for Cd and As. In the dry season, the concentrations of all HMs were slightly higher than in the rainy season, which can be attributed to the fact that pollutants in rivers may be diluted by rainwater, thus lowering the value. Enrichment factor, geo-accumulation index, contamination factor, and pollution load index indicated a high level of contamination by HMs and moderate levels of ecological risk. The hazard index was < 1 for adults and children in both seasons, revealing no possible non-carcinogenic health risk. Hazard Quotient for individual exposure path can be ranked as ingestion > dermal > inhalation for both seasons, regardless of age group. Carcinogenic risk via the entire three exposure path was ascertained safe for adults and children except for ingestion in children for both seasons. However, total carcinogenic risk value indicated low to medium risk for children in both seasons, while it is within a safe limit for adults. Multivariate statistical analysis indicated possible sources were anthropogenic primarily due to untreated wastes discharge from metal and waste dumping sites, oil and refinery industries, and glass and ceramic industries close to the sampling sites of the Shitalakshya river.