The changing climate is a concern to sustainable water resources. This study examined climate change impacts on river discharge seasonality in two West African river basins; the Niger river basin and the Hadejia-Jama’are Komadugu-Yobe Basin (HJKYB). The basins have their gauges located within Nigeria and cover the major climatic settings. Here, we set up and validated the hyper resolution global hydrological model PCR-GLOBWB for these rivers. Time series plots as well five performance evaluation metrics such as Kling–Gupta efficiency (KGE),); the ratio of RMSE-observations standard deviation (RSR); per cent bias (PBIAS); the Nash–Sutcliffe Efficiency criteria (NSE); and, the coefficient of determination (r2), were employed to verify the PCR-GLOBWB simulation capability. The validation results showed from satisfactory to very good on individual rivers as specified by PBIAS (−25 to 0.8), NSE (from 0.6 to 0.8), RSR (from 0.62 to 0.4), r2 (from 0.62 to 0.88), and KGE (from 0.69 to 0.88) respectively. The impact assessment was performed by driving the model with climate projections from five global climate models for the representative concentration pathways (RCPs) 4.5 and 8.5. We examined the median and range of expected changes in seasonal discharge in the far future (2070–2099). Our results show that the impacts of climate change cause a reduction in discharge volume at the beginning of the high flow period and an increase in discharge towards the ending of the high flow period relative to the historical period across the selected rivers. In the Niger river basin, at the Lokoja gauge, projected decreases added up to 512 m3/s under RCP 4.5 (June to July) and 3652 m3/s under RCP 8.5 (June to August). The three chosen gauges at the HJKYB also showed similar impacts. At the Gashua gauge, discharge volume increased by 371 m3/s (RCP8.5) and 191 m3/s (RCP4.5) from August to November. At the Bunga gauge, a reduction/increase of -91 m3/s/+84 m3/s (RCP 8.5) and -40 m3/s/+31 m3/s/(RCP 4.5) from June to July/August to October was simulated. While at the Wudil gauge, a reduction/increase in discharge volumes of −39/+133 m3/s (RCP8.5) and −40/133 m3/s (RCP 4.5) from June to August/September to December is projected. This decrease is explained by a delayed start of the rainy season. In all four rivers, projected river discharge seasonality is amplified under the high-end emission scenario (RCP8.5). This finding supports the potential advantages of reduced greenhouse gas emissions for the seasonal river discharge regime. Our study is anticipated to provide useful information to policymakers and river basin development authorities, leading to improved water management schemes within the context of changing climate and increasing need for agricultural expansion.