The dynamic nature of habitat patches in rivers is driven primarily by flow regime. Altered hydrology, through river regulation, can limit the size and distribution of slackwater patches; important areas for the development of young fish and for shrimp in lowland rivers. Between late October 2002 and late January 2003, we investigated responses of fish, shrimp and their potential prey to the experimental creation of slackwaters and, conversely, to the experimental creation of flowing patches, by diverting water away from flowing patches and into slackwater patches, respectively. A pre-experimental survey indicated that slackwaters contained many more fish than flowing patches, and fish larvae were flushed out of slackwaters during the construction of flowing patches. Creation of slackwaters resulted in increased abundance of fish and shrimp, with the opposite occurring when slackwaters were changed into flowing patches. Converting slackwaters into flowing patches, and vice versa, altered the species composition of zooplankton and microbenthic assemblages but did not change their densities. Thus, standing crop of potential prey alone could not explain the differences in fish or shrimp abundance found between patch types. We hypothesize that slackwaters primarily act as refuges from current and provide energetic advantages to the young stages of fish and to shrimp. River regulation has the potential to affect the recruitment success of fish and shrimp by affecting the size, arrangement and availability of slackwater patches.