Delta outflow directly controls and often dominates the spatial and temporal distributions of most properties and biological processes in the northern reach. The outflow contributes suspended particles, dissolved oxygen, and silicate, and generates an estuarine circulation cell and a turbidity maximum. The circulation pattern and associated features largely dictate spatial distributions. Seasonal changes, however, are caused by relative changes in outflow (which determine water residence time and thus flushing rates) and light-limited biological activity (photosynthesis, nutrient uptake, and oxygen production): during winter, mixing and advection control biological activity, whereas during summer, both biological activity and physical processes are important.

The relation between Delta outflow and biological processes in the southern reach, however, is less direct: biological activity has a relatively greater effect on the spatial and temporal distributions of these properties. Distributions of properties are dominated by the perennial inflow of detritus and nutrient-rich waste water at the southern boundary. These inputs are augmented during winter by discharges from local intermittent streams that may contribute large amounts of nitrogenous compounds. The substrate is the major source of particles and dissolved silicate. Greatest biological activity apparently takes place during spring rather than summer as in the northern reach. This increased activity in the southern reach is caused in part by Delta-outflow induced stratification that tends to maintain algal cells in the photic zone.