Coastal upwelling regimes associated with eastern boundary currents are the most biologically productive ecosystems in the ocean. As a result, they play a disproportionately important role in the microbially-mediated cycling of marine nutrients. These systems are characterised by strong natural variations in carbon dioxide concentrations, pH, nutrient levels and sea surface temperatures on both seasonal and interannual timescales. Anthropogenic changes are superimposed onto this variability: carbon dioxide derived from fossil fuel combustion is adding to the acidity of upwelled low-pH waters; low oxygen waters associated with coastal upwelling systems are growing in their extent and intensity; and nutrient inputs to the coastal ocean continue to increase. Coastal upwelling systems may prove more resilient to changes resulting from human activities than other ocean ecosystems because of their ability to function under extremely variable conditions. Nevertheless, perturbations to primary production and fisheries, loss of biologically-available nitrogen, and changes in fluxes of climate-relevant gases could result from the perturbation of these highly productive and dynamic ecosystems.