<p>Microbially-mediated transformations are important for removing wastewater chemicals in rivers. In-stream degradation rates are likely to be affected by channel morphology and size because these factors determine the extent of chemical contact between the water column and the microbial community in fixed biofilms, where most microbially-mediated processes are expected to take place. We hypothesize that transformation rate constants are inversely proportional to hydraulic radius (<i>R</i>: the ratio of channel cross-sectional area to wetted perimeter). Microbial transformations are also predicted to be controlled systematically by bed sediment characteristics. This will be a function of sediment surface area per unit volume (for biofilm colonisation) and hyporheic exchange. Here, we test the above hypotheses in controlled 14-day laboratory experiments, by monitoring nitrification and biodegradation in stirred tanks with three different water depths and three different sediment sizes (sand, gravel and cobbles). Transformation rate constants were inversely proportional to depth, supporting the notion that channel morphology represents a significant system-specific control. Rate constants for nitrification were highest in the gravel treatments and lowest in sand. This suggests that intermediate grain sizes simultaneously allow good biofilm colonisation and solute exchange between sediment and the water column. There was, however, little difference in biodegradation rate constants between different sediment sizes. This study highlights the need to consider geomorphology in models of chemical exposure.</p>