We conducted field work in South San Francisco Bay to examine cohesive sediment flocculation dynamics in a shallow, wave- and current-driven estuarine environment. Drawing on data collected using a suite of acoustic and optical instrumentation over three distinct seasons, we found that the factors driving floc size variability differed substantially when comparing locally-sourced sediment (i.e., through wave-driven resuspension) to suspended sediment advected from upstream. Statistical analysis of our extensive field data revealed additional seasonal variability in these trends, with wave stress promoting floc breakup during the summer and winter months, and biological processes encouraging floc growth during the spring productive period. Combining these data with fractal dimension estimates, we found that seasonally-varying floc composition can lead to differences in floc settling velocity by a factor of approximately two to five for a given floc size. Finally, by analyzing co-located turbulence and sediment flux measurements from the bottom boundary layer, we present evidence that the relationship between floc size and the inverse turbulent Schmidt number varies with floc structure. These results can be used to inform sediment transport modeling parameterizations in estuarine environments.