Microhabitat preferences of 12 benthic invertebrate taxa were investigated in four New Zealand rivers. Most taxa showed significant habitat preferences. Generally, taxa were more abundant in water less than 0.75 m deep and in gravel or coarser substrates, and no taxa showed a clear preference for fine substrate (sand and fine gravel) or deep water.Coloburiscus humeralis, Zelandoperlaspp., andAoteapsychespp. preferred coarse substrate and water velocities of more than 0.75 m s−1, whereasNesa‐meletusspp. andPycnocentrodesspp. were associated with similar substrate but lower water velocities (0.2–0.8 m s−1). Naididae preferred low (< 0.3 m s−1) water