We built an ecosystem model to emulate changes in the biomass and mortality rates of managed species in South Puget Sound from 1970 to the present and simulate likely changes to the year 2054. Our model simulates historic primary production variation to emulate observed changes in the biomass and mortality of upper trophic level species in South Puget Sound. The emulation of historic dynamics uses time series from monitoring work on many marine species in South Puget Sound including birds, mammals, salmonids, demersal fish, shellfish, eelgrass, kelp and phytoplankton. Time series of resampled historic primary production changes were used to develop forecasting scenarios of potential long-term changes in the biomass of managed species under a variety of fishing and aquaculture policies. Our results suggest that current fisheries and aquaculture policies foster the rebuilding of many managed marine species in South Puget Sound. Our results also suggest that dramatic increases in aquaculture would have little to no effect on the trophic dynamics of most species in South Puget Sound. This modelling work provides a convenient and cost effective way to decide where monitoring resources may best be devoted. Our model identifies which species are more likely to experience significant change to their biomass and/or mortality rates in the future given a variety of natural and anthropogenic sources of change. Our model can also be used to examine how different management policies may attenuate or exacerbate likely dynamics for given species in South Puget Sound