Anthropogenic disturbances such as damming and deforestation degrade riverine ecosystems. Knowledge of reference conditions is required in order to quantify effects of such disturbances. This study assessed habitat and community structure at five sites along an altitudinal gradient in the Layou River, which is the largest river in Dominica and its watershed remains mostly forested. In addition to basic physical and chemical parameters, we quantified macroconsumer (fishes and shrimps) abundance through snorkeling transects and trapping as well as macroinvertebrate biomass using surbers and D-nets. Water pH, conductivity, temperature, and discharge decreased with elevation while canopy cover increased. Macroconsumer dominance shifted from fishes at low elevations to shrimps at high elevations. Macrobrachium heterochirus was present at all sites while M. crenulatum was observed at only the higher three sites. Macroinvertebrate biomass and richness peaked at the mid-elevation site where Ephemeroptera and Trichoptera were most abundant. Our data quantify baseline conditions along the Layou, which can be used to assess effects of future development in the watershed. Community structure and therefore IBI scores, varied dramatically among sites, many of which appeared unaffected by obvious anthropogenic disturbance. This suggests that reference sites of similar elevation and stream size be used when assessing disturbances.