Eastern boundary upwelling systems (EBUSs) support roughly one-fifth of the world’s fish catch. Weak ventilation and high oxygen consumption create an Oxygen Minimum Zone (OMZ) in these areas, which are experiencing climate change, such as ocean deoxygenation, acidification, and warming. Reviewing variations in net primary production(NPP), oxygen concentration, and the underlying dynamics is essential for predicting the health of the EBUS and its impacts on fish availability. In the seasonal cycle, surface chlorophyll (or NPP) in mostly EBUSs grows to peaks in spring or summer. An out-of-phase relationship between seasonal chlorophyll concentrations (or NPP) and upwelling intensity in Peru and Benguela upwelling means other factors like mixed layer depth(MLD), stratification, mesoscale eddy, and filament also constrain the seasonal cycle of chlorophyll (or NPP). Based on the observations in the past three decades, OMZ is westward expanding in most of the EBUSs; NPP is decreasing and varies with latitude. EBUSs exhibit strong coupling between wind-forced upwelling and oceanic (sub)mesoscale dynamics. Eddy-induced subduction of phytoplankton, oxygen, and other tracers through the ageostrophic vertical circulation. Low oxygen and high nitrate water transport offshore by coherent structure(front, eddy). Mesoscale eddies are hotspots of biogeochemical processes, like enhanced respiration and NPP. In the past three decades, not only has the wind-forcing upwelling changed, but also the stability of the upwelling. One case in Peru upwelling and Benguela upwelling shows that wind-forcing upwelling is getting weaker, and the upwelling becomes more unstable, which forces more active eddies and filaments. The change in the intensity and instability of upwelling both impact the biogeochemical processes in EBUSs.