Neotropical cloud forests are a critically endangered ecosystem characterised by their unusual hydrological conditions which frequently make them important sources of clean potable water. To facilitate any meaningful research on cloud forest streams it is necessary to first describe the structure and composition of the local lotic aquatic communities and to establish which environmental factors structure them under natural conditions. The present study sampled the macroinvertebrate communities of rivers draining the montane cloud forests of Cucuso National Park in Honduras, where increasing anthropogenic pressures are threatening water quality. Using multivariate techniques a bottom-up approach was adopted to establish groups of similar sites and identify environmental factors driving the differences between these. Three site groupings emerged based largely on differences in taxon composition driven mainly by pH and altitude.