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An examination was made of the integration of local biological variation within the longitudinal profile of a stream due to patchy hydraulic patterns. Invertebrates were collected monthly in pool, run and riffle biotopes at five sites on a 20-km mountain stream in Northern Italy, running from 1050 to 235 m a.s.l., and showing a good biological status. About 26 000 individuals belonging to 60 different insect taxa were collected and variation in their distribution and abundance were analysed by Principal Component Analysis. The results provide evidence on pool-riffle biological differences and a discussion is included on the taxa unique to each hydraulic habitat. The pool biotope shows a relatively high insect diversity, but separation of biotopes with high current velocity into riffles and runs did not provide further insight on the patterns of insect distribution. Variation in insect taxonomic structure near the mid-point of the stream longitudinal profile was representative of the total longitudinal variation. This suggests that hydraulically fragmented habitats at one particular site can provide information on invertebrate structure that can be extrapolated to sites upstream and downstream of the sampled site.