Since the 1970s, the Niger basin has been characterized by hydro-climatic changes which have significant impacts on local populations. These changes are not well documented as a result of a decreasing observation network for hydro-climatic data. Indigenous peoples’ knowledge has increasingly been considered an important component in addressing these data gaps. We evaluated the consistency of indigenous perceptions and adaptive responses with rainfall and river discharge observations in the Niger basin. Socioeconomic data were collected from 239 households in 30 communities across two settlements in the Niger basin. Data on historical rainfall and river discharge from 1950 to 2010 were analyzed and the consistency with local perceptions was assessed. Generally, there was a high agreement between observations and perceptions, but impacts of climate change in the communities were dependent on social and environmental factors that can introduce differences in perception despite identical observations. Indigenous perceptions gave good indication of the most vulnerable sectors as well as communities who also displayed the greatest willingness to combat climate change. These results suggest that integration of indigenous perceptions into climate change science, especially in data scarce regions, is highly valuable.