Nitrogen (N) and light availability limit phytoplankton growth and hence regulate food supply for mussel farming in Pelorus Sound, New Zealand. In Beatrix Bay, a large 35-m deep embayment off Pelorus Sound, the supply of N is heavily influenced by physical factors. Bottom intrusions of N-rich or depleted oceanic water occur in the main channel of Pelorus Sound and Ndepleted, phytoplankton-enriched Pelorus River water characterises the near-surface low salinity field. Inside Beatrix Bay, nutrient cycling via phytoplankton uptake, sedimentation, and subsequent regeneration from the sediments by mineralisation, also has an important influence on the availability of N in the water column. However, almost continuous salinity or thermally induced density stratification, or both, within Beatrix Bay meant that the upper and lower water columns were often decoupled so that N regenerated from the sediments was not readily available in the upper water column, and phytoplankton settling from the upper water column may not reach the sediments directly below because of large horizontal transport. The N supply in the upper water column of Beatrix Bay, where the mussels are farmed, is most likely regulated by advection in and out of the bay from external sources. Conversely, the N concentrations below the pycnocline could be almost entirely supplied via mineralisation from the sediments. The rates of sediment N regeneration were seasonally dependent. During winter, when sedimentation exceeds mineralisation, N accumulates in the sediments at a rate of up to 10 mg m -2 day -1 , whereas in summer, when mineralisation exceeds sedimenation, N is lost from the sediments at rates of up to 9 mg m -2 day -1 .