Variability in the heavy metal concentrations in aquatic environments may be influenced by a number of factors that may occur naturally or due to anthropopressure. This article presents the risk of contaminating Warta River bottom sediments with heavy metals such as As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, and Zn. Samples collected from 35 sites located along the river course were analysed over the period of 2010–2021. The calculated pollution indices are characterised by significant spatial variability that was additionally subject to changes in subsequent years. The analysis may have also been influenced by individual measurement results that, in extreme cases, may strongly deviate from the concentration values determined in the same site during the remaining years. The highest median concentrations of Cd, Cr, Cu, Hg, and Pb were in samples collected from sites that are surrounded by areas of anthropogenic land use. Samples from adjacent sites to agricultural areas showed the highest median concentrations of Co, Mn, and Ni, and Zn for those adjacent to forest areas. The research results indicate that, when analysing the degree of the risk of contaminating river bottom sediments with heavy metals, it is necessary to take into account long-term variability in metal concentrations. Taking into consideration data from only one year may lead to inappropriate conclusions and hinder planning protective measures.