The main purpose of this study was to evaluate temporal and regional variability of contamination by heavy metals (HMs) in river sediments using their enrichment factors(EFs) and benchmarking according to sediment quality guidelines (SQGs). The Zlin region in the Czech Republic (Morava and Drevnice River basins) represents a model area where several regionally specific ecological risk assessment studies have recently been conducted with a focus on organic pollution, eco-toxicity, geological, and geochemical characteristics.