Negative interactions between corals and algae often are implicated in preventing the recovery of coral-depauperate reefs. However, few studies have explored the effects of environmental conditions on the mechanisms underlying the outcomes of coral–algal interactions. We examined the influence of water flow, a pervasive feature of reefs that is known to affect both coral and algal physiology, on massive Porites algal interactions at different spatial and temporal scales with two types of algal competitors. Outcomes of coral–algal interactions were influenced by both water flow and algal type. Algal turfs outcompeted corals more frequently in low flow conditions, where microbial concentrations were higher, than in higher flow areas. Turbinaria ornata outcompeted massive Porites more often in higher flow and consistently was associated with lower microbial concentrations. This study highlights that outcomes of coral–algal interactions are microhabitat dependent and that water flow limits the effectiveness of some mechanisms of coral–algal competition.