Mussel farming places a benthic organism in a pelagic environment; it is therefore important to understand the driving force that transports the food to the mussels. The hydrodynamic regimes in the sidearms and embayments in Pelorus Sound are dominated by the lunar tide, and a net estuarine circulation in the main channel flowing inwards along the bottom and outwards along the top. Salinity gradients extend throughout the sound from the river inflows, with strongest density stratification in the sidearms and embayments: nearest the head of the sound. There, the water column is separated at the pycnocline into upper and lower layers which tend to move in different directions or at different velocities. Local circulation patterns modify tidal flushing patterns, producing extended residence times in some embayments, whereas other embayments off the side of the main channel tend to be flushed more rapidly by through‐flow water and have shorter residence times than would otherwise be expected. The changing inflow of fresh water modifies the local hydraulic regimes in the inner sounds, especially during flood conditions.