The alternative hypothesis that observed regions of recurrent hypoxia on the New Jersey inner shelf are more related to coastal upwelling than riverine inputs of nutrients was investigated through a series of multidisciplinary research programs beginning in 1993. The largest variations in ocean temperatures along the New Jersey coast, other than seasonal, are found to be caused by episodic summertime upwelling events driven by southwesterly winds associated with the atmospheric Bermuda High. Off the southern coast of New Jersey, topographic variations associated with ancient river deltas cause upwelled water to evolve into an alongshore line of recurrent upwelling centers that are colocated with historical regions of low dissolved oxygen. Recurrent upwelling centers are observed every summer in a 9-year data set. The most significant upwelling events occur in summers following colder than usual falls and winters. Size and duration of individual events are correlated and are found to depend on the wind forcing history that effects the inner side of the Middle Atlantic Cold Pool, the precipitation history that effects the strength of the Hudson River plume, and the mixing storm frequency. Upwelling results in a significant enhancement of particulate organic carbon. The typical carbon enhancement associated with the upwelling is sufficient to deplete 75% of the oxygen in the bottom water, making it borderline hypoxic. This indicates that topographically controlled coastal upwelling, rather than riverine inputs, is the more probable mechanism for generating the historical regions of recurrent hypoxia observed along the New Jersey coast.