The Eastern Boundary Upwelling Systems (EBUS) are highly productive ecosystems globally, contributing approximately 20% of the world’s fishery resources and bearing significant ecological and socioeconomic importance. These EBUSs are primarily influenced and sustained by seasonal equatorward wind patterns. Along the Atlantic coast of Morocco, there are two distinct and persistently occurring upwelling patterns: a robust one to the south of (26°N) and a weaker one to the north. In this study, we present a coastal upwelling (transport) index based on combined contributions from both Ekman and Geostrophic transports, complemented by a recently refined thermal upwelling index based on sea surface temperature (SST). The seasonality patterns of these indices align with earlier research findings, revealing a sequence of wind-to-chlorophyll-to-SST lag relationship at all latitudes (24°N, 27°N and 32°N) during the period from 1993 to 2021. Subsequently, the two indices and Chlorophyll-a signature and three potential basin-scale driving factors, the North Atlantic Oscillation (NAO), the Azores High and the East Atlantic Oscillation (EAO) are analyzed to explore the interannual variability of the upwelling system and connect them to those of the prevailing wind patterns. Our analysis reveals three prominent periodicity bands: one near-decadal cycle spanning 8–10 years and two interannual cycles of 4–5 years and 2–3 years. It appears that the interannual bands are influenced by variations in the amplitude of the Azores high center pressure and are associated with the EAO, while the near-decadal cycles may be linked to the NAO. Furthermore, our examination of extreme events suggests that high (low) upwelling years tend to coincide with low (high) EAO years.