The influence of density stratification on sedimentation, suspension, and resuspension in Tasman Bay and Beatrix Bay, New Zealand, two contrasting coastal environments, was studied with specific reference to the implications for modelling aquaculture sustainability. Tasman Bay, an enhanced scallop (Pecten novaezelandiae Reeve) fishery, is a very large coastal indentation gently shelving to c. 20 m deep c. 10 km from shore and open to the Tasman Sea, whereas Beatrix Bay, an area of intense Greenshell™ mussel (Perna canaliculus Gmelin) aquaculture, is a small (22 km2 × 30–40 m deep) enclosed embayment off the side of the nearby Pelorus Sound. Sediment trap arrays were used to determine the vertical fluxes of suspended solids and the associated chlorophyll component. Benthic chambers were used to investigate sediment nutrient regeneration. In summer, salinity gradients in both bays are minimal or non‐existent because of low inputs of fresh water and density stratification is mainly controlled by water temperature. The data from mid summer exhibited different spatial distribution patterns for detritus and phytoplankton biomass (as indicated by chlorophyll) in these two very different bays, although they had similar turbulent environments. The density discontinuity at the thermocline had a strong influence on settling of phytoplankton. There was evidence of upwards entrainment of suspended paniculate matter into the upper water column from the thermocline in Beatrix Bay. Benthic resuspension was estimated to contribute up to 90% of the suspended solids caught in sediment traps near the sea floor in both bays. The trapping rate of phytoplankton was thought to be dependent on species dominance. Possible mechanisms of resuspension included turbulence in the benthic boundary layer, and high velocities below the thermocline associated with internal seiches. The presence of a mid water column chlorophyll maximum in Beatrix Bay is discussed in terms of nutrient and light regimes at the thermocline, and species composition. In Tasman Bay, the chlorophyll maximum was thought to be caused by resuspension of benthic microphytes and their subsequent confinement in a thin layer (2–4 m thick) of high turbulence between the thermocline and the seabed.