Data from runs in 88 rivers throughout New Zealand, and a comparison between areas of contrasting substrate size in the Mohaka River, were used to investigate the influences of physical factors on benthic macroinvertebrates. Substrate size preferences were more clearly demonstrated by the comparison of different substrates in the Mohaka River than between runs in the 88 rivers. Taxonomic richness and densities of most collector‐browsers were highest on small cobble‐boulder substrates. However, filterers and a facultative shredder showed strong preferences for large cobbles and boulders and an undescribed orthoclad showed a strong preference for sand. Among the 80 stony‐bedded rivers, those exposed to maximum flows of < 5×, 5–10×, and 10–20× their median flow during 6 weeks before sampling had similar taxonomic richness, densities, and biomass. In contrast, rivers that had experienced maximum flows of > 20× their median flows had markedly lower median taxonomic richness, density, and biomass than less‐flooded rivers. Among the 51 stony, “non‐flooded” sites, those with 1–30% of their catchments developed to improved pasture had similar community composition to, but higher total biomass than those with < 1% development. However, sites with > 30% catchment development (median = 70%) differed significantly (P< 0.1) from those with less developed catchments: the former had lower diversity, taxonomic richness, numbers of ephemeropteran, plecopteran, and trichopteran species (EPT), and had lower biomass of species that are sensitive to changes in water quality related to eutrophication; they had higher biomass of species that are associated with an abundance of periphyton. Trout biomass was also c. 3‐fold lower than in the rivers with lesser‐developed (1–30%) catchments.