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Abstract Fluid (air or water) movements are key determinants of living systems from cellular to community levels of organization. Water flow can influence individual fitness and local population dynamics, but less is known about the collective response of natural communities to alteration in water flow because parameter responses to flow may be additive, juxtaposed, or interactive. To examine how changes in water flow affected initial larval settlement patterns of epifaunal and infaunal animals, colonization of larger individuals, and prey survival, we manipulated water flow (−50% or +47%) in situ using large wooden channels over small experimental oyster reefs. To test whether initial settlement patterns were additive or influenced by early post‐settlement processes (i.e., predation or competition reduced the densities), we compared patterns in short‐duration trials (two weeks) to those in longer duration deployments (six weeks). We found that minor changes in water flow (5–10 cm s−1) resulted in large changes in settlement of many species, predation levels, and the modification of initial settlement patterns. Settlement (two‐week intervals) and subsequent recruitment (six‐week intervals) increased for several species as flow rate increased. For most species, this relationship peaked at mid‐level flows (mud crabs, barnacles, and bivalves), whereas others (oysters) continued to increase with higher flow rates. Settlement patterns were best preserved in recruitment under high flow conditions where post‐settlement mortality was lower. Collectively, our results demonstrate how biological and physical processes are coupled in oyster reef systems, with relatively minor changes in water flow affecting pre‐ and post‐settlement processes.