Cobscook Bay, at the mouth of the Bay of Fundy, exhibits extraordinary natural productivity and ecological richness that has been recognized for millennia. The co-existence of so many remarkable ecological attributes is of both practical and scientific interest and has intrigued researchers for over a century. Nevertheless, the question of why this high productivity and species richness should co-occur in this mid-latitude Bay has not been addressed on an ecosystem level. A grant from the Andrew W. Mellon Foundation through The Nature Conservancy allowed an interdisciplinary, multi-institutional team of marine scientists to investigate the physical, chemical, geological, and biological dynamics of the Bay in an integrated ecosystem context. This special issue of the Northeastern Naturalist presents the results of original field research on the physical forcing functions at work in the Bay and the contributions of the principal primary producers. This knowledge is combined with historical information into an energy systems model and emergy analysis that describes the flows of materials and energy through the system and allows comparisons with other estuarine systems.