The acid volatile sulphide (AVS) and simultaneously extracted metals (SigmaSEM) method is increasingly used for risk assessment of toxic metals. In this study, we assessed spatial and temporal variations of AVS and SigmaSEM in river sediments and floodplain soils, addressing influence of flow regime and flooding. Slow-flowing sites contained high organic matter and clay content, leading to anoxic conditions, and subsequent AVS formation and binding of metals. Seasonality affected these processes through temperature and oxygen concentration, leading to increased levels of AVS in summer at slow-flowing sites (max. 37micromolg(-1)). In contrast, fast-flowing sites hardly contained AVS, so that seasonality had no influence on these sites. Floodplain soils showed an opposite AVS seasonality because of preferential inundation and concomitant AVS formation in winter (max. 3-30micromolg(-1)). We conclude that in dynamic river systems, flow velocity is the key to understanding variability of AVS and SigmaSEM.