Data-driven forecasts and simulations for Massachusetts Bay based on in situ observations collected during August – September 1998 and on coupled four-dimensional (4-D) physical and biogeochemical models are carried out, evaluated, and studied. The real-time forecasting and adaptive sampling took place from August 17 to October 5, 1998. Simultaneous synoptic physical and biogeochemical data sets were obtained over a range of scales. For the real-time forecasts, the physical model was initialized using hydrographic data from August 1998 and the new biogeochemical model using historical data. The models were forced with real-time meteorological fields and the physical data were assimilated. The resulting interdisciplinary forecasts were robust and the Bay-scale biogeochemical variability was qualitatively well represented. For the postcruise simulations, the August – September 1998 biogeochemical data are utilized. Extensive comparisons of the coupled model fields with data allowed significant improvements of the biogeochemical model. All physical and biogeochemical data are assimilated using an optimal interpolation scheme. Within this scheme, an approximate biogeochemical balance and dynamical adjustments are utilized to derive the non-observed ecosystem variables from the observed ones. Several processes occurring in the lower trophic levels of Massachusetts Bay during the summer – autumn period over different spatial and temporal scales are described. The coupled dynamics is found to be more vigorous and diverse than previously thought to be the case in this period. For the biogeochemical dynamics, multiscale patchiness occurs. The locations of the patches are mainly defined by physical processes, but their strengths are mainly controlled by biogeochemical processes. The fluxes of nutrients into the euphotic zone are episodic and induced in part by atmospheric forcing. The quasi-weekly passage of storms gradually deepened the mixed layer and often altered the Bay-scale circulation and induced internal submesoscale variability. The physical variability increased the transfer of biogeochemical materials between the surface and deeper layers and modulated the biological processes.