Macroinvertebrates were collected and in-stream habitat assessed at 19 sites in the River Raisin watershed in southeastern Michigan, USA. Sites were located throughout three distinguishable areas of the watershed based on topography, geology and land use . The intensity of agriculture, the predominant land use in the watershed, varied markedly among these three areas. Relationships between macroinvertebrate assemblages and habitat variables were explored by canonical correspondence analysis (CCA), a mul tivariate statistical technique. The Habitat Quality Evaluation Index (HQEI), mean bank condition, and the proportion of fine substrate explained most of the variation among the sites in macroinvertebrate presence and abundance. The analysis grouped sit es in the upper watershed, but sites in the mid-watershed and lakeplain areas did not separate. In addition, TWINSPAN was used to classify sites into four groupings based on similarities in macroinvertebrate composition, and again based on 10 in-stream h abitat measures. Thirteen of the 19 sites were classified similarly at the first or second TWINSPAN divisions for macroinvertebrate and habitat data sets. Both the CCA and TWINSPAN analysis show some correspondence between in-stream habitat and macroinv ertebrate fauna. The lack of correspondence between in-stream habitat and macroinvertebrates at several sites in the TWINSPAN classification may indicate that regional influences override local habitat conditions.