The Kosva Bay is permanently affected by acid mine drainage (AMD) from Kizel Coal Basin in the Perm Krai of Russia. This discharge is released in the middle part of the Kosva River from the abandoned mines. This study investigates the current trace element (TE) concentrations for Zn, Cu, Pb, Ni, Cr, Cd, As, and Hg and the mineral composition, major oxides, grain size of sediments, and acute toxicity using two test organisms within the site of AMD downstream from the Kosva River and up to the Kosva Bay of Kama Reservoir. The objectives of this study were to analyze the quality of sediment and level pollution of Kosva Bay using pollution and ecotoxicological indices. The environmental indices, namely the contamination factor (CF), the geoaccumulation index (Igeo), and the potential ecological risk factor (Eri), indicate contamination by Cr and Pb in sediments at the site of AMD, with the highest values for Cr, Cu, and As in the Kosva Bay sediments downstream of abandoned coal mines. The results of Igeo and CF average values in bay of sediments showed different degrees of contamination, from moderate contamination to considerable contamination, respectively. According to the potential ecological risk index (RI) values, the Kosva Bay sediments exhibited low to moderate risk, and As and Cd have the highest contribution rate. According to LAWA and the Polish geochemical classification of sediments, sediments of the bay correspond to the highest levels (IV–III classes) for Cr, Ni, and Hg. Based on the SQGC, Hg, Cd, Cr, and Ni are the most probable for resulting in adverse effects on aquatic organisms in this study. The results of this study indicate that complex pollution and ecotoxicological indices must be supported by ecotoxicologal tests. High precipitation totals, low evaporation rates, and flow regulation stream by the Shirokovsky Reservoir located upstream from abandoned coal mines provide significant fluctuations in streamflow, which is probably the most important factor controlling the distribution and mobility of TE in the studied sediments.