A study of microhabitat use by fourteen abundant fish species was undertaken in the lower Ntem River Basin in Cameroon (Africa). Seventy-one microhabitats including pools, raceways and riffles were studied twice during the 1994 and 1995 dry season. Results obtained by Canonical Correspondence Analysis (CCA) showed a good niche separation along the ordination axes I (λ1 = 0.37) and II (λ2 = 0.20). Microhabitat selection by these species reflects response to several physical factors including width, depth, current velocity and substrate type. However, a substantial part of the variation in species segregation was explained by both instream (% leaves, woods and roots, and aquatic plants) and bankside (% mean canopy closure) cover. A striking pattern encountered during this study was the frequent size-related variation in habitat use displayed by many species. For example, smaller individuals of Brycinus longipinnis, Barbus camptacanthus, Distichodus notospilus, and D. hypostomatus, occurred more often in faster flowing waters than did their larger conspecifics. The association displayed by CCA was high (0.957 and 0.938, respectively for the first and second axis), and Monte Carlo test (99 permutations) revealed that these associations were significantly different from random (p = 0.01). The implications of these results for habitat management are discussed.