The aim of this research is to assess the effects of oil palm plantations on stream habitat and their fish assemblage diversity. We hypothesize that streams which drain through oil palm plantations tend to be less heterogeneous, limiting the occurrence of many species, than streams that drain through forest fragments, which support higher fish diversity. A total of 17 streams were sampled; eight in forest fragments and nine in oil palm plantations. Environmental and biological variables were sampled along 150 m stretch in each stream. Of the 242 environmental variables measured, ten were considered important to assess the condition of structural habitat, and out of these variables, four were considered relevant in the distinction between streams in oil palm plantations and forest fragments. A total of 7245 fishes were collected, belonging to 63 species. Unlike our original hypothesis, the species richness did not differ between forest fragment and oil palm plantations streams, showing that it is not a good divert measure in streams disturbance assessment. However, fish assemblages differed in species composition, and 56 species were recorded in oil palm plantation streams, while 44 species were recorded in forest fragments streams. Some species were identified as indicators of either altered (Aequidens tetramerus and Apistogramma agassizii) or undisturbed areas (Helogenes marmoratus). Overall, oil palm plantations were proven to change stream habitat structure and fish species distribution, corroborating other studies that have evidenced changes in patterns of biological community structure due to impacts by different land uses.