Nutrient mass balance analyses are a way of obtaining 'whole system' viewpoints on coastal biogeochemical functions and their forcing. Seasonal mass balances are presented for four large bay systems in New Zealand (NZ), with the aim of showing how they can inform coastal management. Freshwater volumes, and surface and groundwater, wastewater and atmospheric inorganic and organic nitrogen (N) and phosphorus (P) were balanced with levels of salinity, N and P from ocean surveys, used to determine non-conservative N and P fluxes and, via stoichiometry, carbon (C) fluxes. For Golden and Tasman Bays and Hauraki Gulf, exchange with adjacent shelf waters usually dominated total N supply (80-85%). In contrast, for the Firth of Thames, 51% of total N and 85% of dissolved inorganic N supply originated from its agricultural catchment. Net ecosystem metabolism (NEM; balance of autotrophy and heterotrophy) of Golden and Tasman Bays and Hauraki Gulf was usually nearly balanced. In contrast, Firth NEM was highly seasonally variable, often exhibiting strong heterotrophy coincident with expression of respiration-related stressors (low O 2 and high DIC/low pH). Denitrification accounted for about 51% of total N export across the four systems, signifying its importance as a eutrophication-regulating ecosystem service. Budgets made 12 years apart in the Firth showed decreased denitrification efficiency, coincident with large increases in system N and phytoplankton. The findings for land-ocean nutrient balance, NEM and denitrification showed how mass balance budgeting can inform coastal management, including inventories of nutrient inputs, balances of oceanic and terrestrial nutrient loading, and potential for risk associated with biogeochemical responses.