In regulated rivers, environmental flows (the provision of water to maintain ecosystems) are the main management technique used to ameliorate the ecological effects of flow alteration. In addition to altered flow regimes, increased bed sedimentation is also frequently associated with lower flows in regulated rivers. We tested the separate and combined effects of altered flow and river bed sediments (colmation) on benthic invertebrates in twelve flume mesocosms at the Freshwater Biological Association’s River Laboratory in Dorset, UK. Each mesocosm contained two bed sediment types; clean sediment in the upstream section and experimentally colmated (EC) sediment (10% by weight of fines) in the downstream section. Two flow rates were initially established equally amongst the twelve mesocosms, a higher flow rate to create turbulent flow and the lower flow rate to create a transitional flow between turbulent and laminar flows. After 30 days invertebrates were sampled and the flow in six of twelve mesocosms was reversed. The experiment was finalised after sampling invertebrates at day 70. We demonstrated that the addition of fines to stream sediment and the alteration of flow affected benthic macroinvertebrate composition. However, higher flows did not ameliorate the effects of added fines. It is possible that the differences between the turbulent and transitional flow regimes (and their alteration) in the mesocosms was not great enough to create enough shear stress or power to remove fines or alter sediment dynamics.