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Summary Proliferations of periphyton associated with the ecological degradation of streams have been linked to changes in flow regime, most frequently as a product of water abstraction and impoundment. We used descriptive and experimental studies to examine the relationship between water velocity and the distribution of two distinct, often high biomass, periphyton patch types and associated macroinvertebrate communities in the Waipara River, a meso‐eutrophic stream in Canterbury, New Zealand. One patch type (‘Phormidium’) consisted mainly of two filamentous cyanobacterial taxa: a Phormidium/Lyngbya complex and Oscillatoria. The other type (‘filamentous greens’) consisted mainly of several filamentous chlorophyte taxa (Mougeotia sp.) along with various diatom epiphytes. Ash‐free dry mass, chlorophyll a and particulate N and P concentrations were significantly greater in the Phormidium than in the filamentous green patches. There was a significant relationship between patch cover and water velocity, with filamentous greens negatively associated with velocity and dominant in areas with a velocity <∼0.20 m s−1, while Phormidium was dominant at velocities >∼0.40 m s−1. A 7‐day experimental reduction in velocity in Phormidium‐dominated habitats resulted in a significant reduction in% cover (84–21%) with a corresponding increase in filamentous greens (16–79%). There was a small but significant reduction in the % cover of filamentous greens (90–82%) with experimentally increased velocity, but no significant change in Phormidium cover (7–2%), perhaps due in part to the slow growth rate of taxa in this patch type. Characterisation of macroinvertebrate assemblages collected from Phormidium and filamentous green patches and the substratum immediately below showed patch‐specific assemblages, although patch type was a less important determinant than vertical location, with 85% of the macroinvertebrates found in the substratum below algal mats. The differential responses of Phormidium and filamentous green patches to velocity are considered in the context of a subsidy‐stress model that examines how trade‐offs between flow‐mediated biomass accrual and loss processes vary for different algal growth forms. Collectively, these results indicated that key ecological characteristics of rivers can be quite sensitive to spatial and temporal variations in hydraulic conditions that are much smaller than those typical of floods and droughts.