The Chesapeake Bay, while a significant habitat for fisheries resources, is in actuality an aquatic “bedroom community”, as many of the economically important species are seasonally transient. The pressure on these resources due to their demand for human consumption and recreation, proximity to extensive industrial activity along the shores, and climate scale environmental fluctuations has resulted in stock declines by most important species. Our inability to separate natural population fluctuations from those of anthropogenic origin complicates management efforts. The only way to make these separations, and subsequent informed management decisions is by supporting long-term stock assessment programs (monitoring) in the Bay which allow us to examine trends, cycles and stochastic processes between resource and environment. These programs need to monitor both recruitment and fishing mortality rates of the economically important species, and to identify and monitor the environmentally sensitive “canary” species.