Upper Silesia is the most transformed by humans of the Polish territories. As a result of mining, urbanization and other industrial activities, irreversible changes have taken place in the environment. In this paper, the method of collecting, preserving, storing and preparing samples from four Silesian rivers was optimized. Silesian sediment and river water samples are a challenge for the analyst, because they have complex matrices and high content of chlorides coming from the discharges of saline water. This study concerned determination of Sb(III), Sb(V), As(III), As(V), MMA, DMA, AB, Cr(III) and Cr(VI) with high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS). The following columns were used: Dionex Ion Pack AG7 to determine chromium forms, Hamilton PRP-X100 to separate antimony species and Dionex Ion Pack AS7 to determine five chemical arsenic forms. The methodology used allowed for elimination of interferences during analysis of highly saline and complex samples and ions separation directly without adding any complexing compounds. Depending on the analytes, full separation was obtained within 3–9.5 min. The sediment sample extraction and determination were validated (recovery, limit of detection, repeatability and uncertainty) with the certified reference materials (CRMs). The optimized methodology allowed for study of mobility and seasonality changes of As, Sb and Cr species in the river environment.