Coal slag and ash, obtained from burning coal in a textile factory in Duga Resa (Croatia) was discharged directly into the Mrežnica River for 110 y (1884–1994), from where it travelled to the Korana River and further to the Kupa River at Karlovac, a total of ~50 km from its source. Of 54 elements determined by inductively coupled plasma mass spectrometry (ICP-MS) in the <2 mm sediment fraction, a number of anomalously high levels were recorded. The geoaccumulation index (Igeo) for the anomalous elements were: Hg (1.88), B (4.05), Na (1.44), Al (2.05), V (1.65), Cr (1.20), Fe (1.18), Ni (2.10), Cu (2.37), Sr (0.97), Zr (3.27), Mo (3.34) and U (4.03). Low-field magnetic susceptibility (MS) was measured for each sample. The Igeo for MS in the anomalous region is 5.85. Correlation analysis showed good correlation (>0.90) of MS with: B (0.96), U (0.95), Zr (0.94), Sr (0.93), Na (0.92), Mo (0.92) and Ni (0.90). Cluster analysis of R-modality indicates that MS is linked to B, Mo, Na and U. Low correlation of MS with Fe (0.36) suggests that Fe in stream sediments is not in a ferromagnetic form. Neither maghemite, nor magnetite phases were identified by X-ray diffraction (XRD) in the sediments. Low-field magnetic susceptibility provides an indicator of contamination of river sediments by transported coal slag and ash, although it cannot be prescribed to a single element.