A broadscale survey of 118 streams was made throughout New Zealand's South Island to establish relationships between aquatic bryophytes and selected environmental variables. Bryophytes were found in 95 of the streams examined, and covered large areas of the substratum (mean cover of 17%, maximum cover of 86%). TWINSPAN analysis revealed the existence of five sample groupings, of which one supported no bryophytes. Streams without bryophytes typically flowed through developed catchments (pasture or pine) composed of easily eroded rocks. Nutrient levels were high in these streams, and low‐flow events were also common. Streambed stability was low, reflecting lack of stable bedrock and boulder substrata. TWINSPAN identified two major groups of streams with bryophytes: those supporting mosses and those supporting liverworts. These streams differed from those without bryophytes by having a higher streambed stability, and fewer low‐flow events. These two variables thus appear fundamental in controlling aquatic bryophyte distribution patterns. Flood events had no significant impact on these plants once they grew on stable substrata. No differences in stream stability, or substrate composition, were found between streams dominated by mosses and those dominated by liverworts. Catchment geology, land use, water quality, and the number of high‐flow events differed between these streams, suggesting that these factors influenced what type of bryophyte community occurred.