This study investigated the quality of Kupa River sediment using sequential extraction, ecological risk, and contamination indexes (Risk assessment code, Index of geoaccumulation, Enrichment factor, Ecological risk factor, Ecological risk index), determination of magnetic susceptibility of sediments, and statistical methods. The BCR sequential extraction technique was used for evaluating various element-binding forms. Most of the elements were considered to be immobile due to the high availability in the residual fraction. Lead was present mainly in the reducible fraction, while more easily mobile and bioavailable forms were predominant for cadmium and barium. Sediment samples from the river catchment exhibited low ecological risk. The most toxic element, Cd, is the main contributor to the total potentially ecological risk. Increased values of contamination factors have been observed for Zn, Cr, and Ba in some localities. Results of the comparison of element contents in sediments in a 15-year period (2018 vs. 2003) indicated that the situation with toxic element content in sediments along Kupa River improved formost of its course. Unfortunately, on the lower course of the river, the situation has worsened. Using the example of Kupa River sediments, it was shown that the magnetic susceptibility method is excellent indetecting increased values of Cr.