Adequate tools to assess aquatic ecosystems health by bioassessment methods are lacking in Africa. These methods are critical for a suitable management of waterbodies and its related resources to further insure food security. Therefore the present study aims to improve knowledge on freshwater fish communities and their exploitation to assess the ecological status of aquatic ecosystems in Burkina Faso. This is the first time the relationship between fish and their habitat is investigated. More than 40,000 fish specimens were collected from nine sampling areas of the Volta catchment. Besides, 16 habitat characteristic variables and 17 environmental pressure variables were measured. Altogether, 79 fish species belonging to 19 families were identified. The common species were Barbus macrops, Brycinus nurse, Barbus ablabes, Oreochromis niloticus, Sarotherodon galillaeus and Coptodon zillii. The highest species richness was recorded in Nazinga. The electric fishing method collected more species in a mesohabitat, while the end of the rainy season was the suitable period to record higher species richness. Factors such as conductivity, dissolved oxygen, rocks and shading are habitat factors that mostly affect fish assemblages. Pressure variables were assigned into agricultural-, hydrological-, morphological-, water quality-, river connectivity- and exploitation pressure. A global pressure index called Burkina Pressure Index (BPI) is calculated accordingly by taking additive effects of multiple pressures into account; and categorized into three classes (Low, medium and high). Candidate fish metrics reacted on pressure intensity. Especially the species richness and the biomass decreased with high pressure while percentage of dwarf species increased. Modern strategies of ecological assessment tools will be promoted, since such actions will contribute to sustainable management of resources like fisheries that will support social development and poverty reduction.