High resolution time-series of physical and bio-optical data were obtained using moored and bottom-mounted instruments on the southern New England continental shelf during the Coastal Mixing and Optics (CMO) experiment from July 1996 through June 1997. The most prominent physical and bio-optical signals observed during the experiment were associated with the seasonal variability. However, several important events interrupted the seasonal cycle. These episodic events appear to have had a great impact on biogenic and non-biogenic matter. Hurricanes and storms passed over or near the CMO site, resulting in reduced stratification of the water column, particle redistribution, and sediment resuspension. Changing hydrographic conditions that resulted from the influence of several water mass intrusions greatly affected particle concentration on time-scales of days to several weeks. The bottom boundary layer had an influence on particle movement in the water column and along the seafloor. The results suggest that there is likely considerable interannual variability in both the physics and bio-optics on this continental shelf because of active and diverse physical forcing. This experiment also sets the context for comparing our coastal ocean results with previous open ocean findings. Important differences arise because of coastal bottom boundary layer effects, large-scale water mass intrusions, and the relatively greater role of tides on the shelf. Time-scales of optical variability are thus generally shorter for the coastal environment.