Abstract Along the coast of North-West Africa, fish supply is important at both socio-economic and cultural levels while threatened by climatic changes. To assess the impact of climate change on the distribution of small pelagic fish, a comprehensive trend analysis was conducted using data from 2,363 trawl samplings and 170,000 km of acoustics sea surveys spanning the period 1995–2015. The approach included estimating eight northern small pelagic species' presence and acoustics spatial distribution of the sardinella. The analysis incorporated key environmental variables, including sea temperature, chlorophyll-a concentration, and a wind-based Ekman upwelling index. The Southern Canary Current Large Marine Ecosystem (CCLME) was divided into five distinct ecological areas, extending from Morocco to Senegal, providing a spatialized perspective on the dynamic changes unfolding within these characteristic areas. Then, yearly averages of the monthly data per area were calculated. Strong warming is reported in all five areas. Over 34 years, from 1988 to 2021, several discernible trends emerged, with the southern CCLME experiencing increases in both wind speed and upwelling intensity, particularly in areas where the coastal upwelling was already the strongest. Despite upwelling-induced cooling mechanisms, sea surface temperature increased in most areas, indicating the complex interplay of climatic-related stressors in shaping the marine ecosystem. Concomitant northward shifts in the distribution of sardinella and other species were attributed to long-term warming trends in sea surface temperature (SST). As a result, the abundance of Sardinella aurita, the most abundant species along the coast, has increased in the subtropics (north part) and fallen in the intertropical region (south part). Independent environmental and ecological observational time series confirm a northward shift of around 180 km in one decade for S. aurita, while S. maderensis did not move significantly. Spatial shifts in biomass from 30 to 145 kilometers were observed for six other exploited small pelagic species, similar to those recorded for surface isotherms. An intensification in upwelling intensity within the northern and central regions of the system is documented without change in marine primary productivity. In contrast, a stable upwelling intensity is reported in the southern region (Senegal), which is associated with a decline in primary productivity. These environmental differences were associated with several small pelagic species beyond national boundaries whose recent overexploitation adds a new threat to their sustainable future in the whole region. Such changes must motivate common regional policy considerations for food security and sovereignty in all West African countries sharing the same stocks.