This study analyses fish assemblages and their habitat use in the Upper Nakambe catchment of Burkina Faso located in the central part of West Africa. The study gives an overview on the available habitat conditions and their effect on fish community composition and abundances as well as on habitat use of single species. Furthermore the conducted fishing methods, electric fishing and the traditional cast net fishing are compared and their pros and cons are discussed. To answer these questions we sampled 157 fish habitats, caught 18,335 individuals and recorded a total number of 16 families, 35 genera and 70 species in four different river reaches. There are lists provided with the spatial distribution of the caught species, ranges for different habitat parameters and usage curves of four key species; i.e. Labeo cubie shows a coarser substrate usage than Bagrus bajad; and the habitat of Chelaethiops bibie exhibits high occurrences for Xylal. The results of this research make important contribution to general knowledge on habitat use and ecology of fish in semi-arid areas of Africa. They can be used as a management tool for a healthy ecosystem and a sustainable fishery which in turn contributes to food security.