Marine heatwaves (MHWs) represent an increasing threat to marine ecosystems, yet their dynamics remain poorly documented in tropical eastern boundary upwelling systems, where upwelling reaches its maximum in boreal winter rather than in summer. This study analyses the spatio-temporal variability of MHWs, their physical drivers, and biological impacts in the Senegalo–Mauritanian Upwelling System (SMUS) over 1982–2024, using satellite-derived SST, chlorophyll-a, and atmospheric reanalysis data.</p> <p data-start="499" data-end="1103">A strong spatial heterogeneity is observed, with the highest cumulative number of MHW days (up to 50 days per year) occurring in shallow regions weakly influenced by upwelling, as well as in offshore transition zones. In contrast, lower occurrences (around 25 days per year) are observed in persistent upwelling areas, particularly at Cap Blanc and along the Petite Côte, which act as relative thermal refuges. At the seasonal scale, MHWs are more frequent and more persistent during the CP, particularly south of 18°N, while their intensity is modulated by the seasonal migration of the upwelling front.</p> <p>Over the 42-year period, the Grande Côte region emerges as the most vulnerable coastal zone, showing the strongest increase in MHW occurrence, with significant trends (p < 0.05) in total MHW days (+10.25 days per decade) and duration (+2.22 days per decade). Along the Petite Côte, trends are approximately four times stronger during the CP (+5.16 days per decade) than during the warming period (+1.34 days per decade). No significant long-term trend is detected for maximum intensity at the annual scale. However, a significant seasonal increase (+0.16 °C per decade) is identified during the warming period in the Grande Côte region. Cap Blanc shows remarkable stability across all indicators, highlighting the buffering capacity of permanent upwelling.</p> <p>Composite analysis of 283 MHW events identifies wind relaxation as the primary driver, reducing Ekman pumping and weakening upwelling circulation. However, the oceanic response differs strongly between regions. In the northern SMUS (Cap Blanc), where upwelling is quasi-permanent, MHWs are moderate and adjust rapidly, reflecting a thermodynamically dominated regime. In contrast, in southern regions with seasonal upwelling, wind relaxation leads to a near-complete collapse of upwelling, resulting in stronger and more persistent heat accumulation, characteristic of a dynamically controlled regime.</p> <p>These physical contrasts translate into distinct biological responses. In the southern SMUS, MHWs lead to a systematic decrease in chlorophyll-a (up to −2 mg m⁻³). In contrast, Cap Blanc exhibits a season-dependent response, with an increase in biomass (up to +3 mg m⁻³) during the CP, sustained by residual nutrient supply and moderate warming, and a decrease in biomass (up to −2.7 mg m⁻³) during the warming period due to enhanced stratification.</p> <p>These results highlight the crucial role of local upwelling dynamics in modulating the characteristics of MHWs and their ecological impacts in this marine ecosystem of major socio-economic importance.