Coastal upwelling regions, which are affected by equatorward-wind variability, are among the most productive areas of the oceans. It has been suggested that global warming will lead to a general strengthening of coastal upwelling, with important ecological implications and an impact on fisheries. However, in the case of the Iberian upwelling, the long-term analysis of climatological variables described here reveals a weakening in coastal upwelling. This is linked to a decrease of zonal sea level pressure gradient, and correlated with an observed increase of sea surface temperature and North Atlantic Oscillation. Weakening of coastal upwelling has led to quantifiable modifications of the ecosystem. In outer shelf waters a drop in new production over the last 40 years is likely related to the reduction of sardine landings at local harbors. On the other hand, in inner shelf and Ria waters, the observed weakening of upwelling has slowed down the residual circulation that introduces nutrients to the euphotic layer, and has increased the stability of the water column. The drop in nutrient levels has been compensated by an increase of organic matter remineralization. The phytoplankton community has responded to those environmental trends with an increase in the percentage of dinoflagellates and Pseudonitzschia spp. and a reduction in total diatoms. The former favors the proliferation of harmful algal blooms and reduces the permitted harvesting period for the mussel aquaculture industry. The demise of the sardine fishery and the potential threat to the mussel culture could have serious socio-economic consequences for the region.