Mass balances on 10 polycyclic aromatic hydrocarbons (PAHs) in the New York-New Jersey Harbor (hereafter "the Harbor") were constructed using monitoring data from the water column, sediment, and atmosphere. Inputs considered included tributaries, atmospheric deposition, wastewater treatment plant discharges, combined sewer overflows (CSOs), and stormwater runoff. Removal processes examined included tidal exchange between the Harbor and the coastal Bight and Long Island Sound, volatilization, and accumulation or burial of sediment-bound PAHs in the Harbor. The PAHs investigated were fluorene, phenanthrene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, perylene, benzo[ghi]perylene, indeno[1,2,3-cd]pyrene, and dibenz[a,h]anthracene. The results show inputs and outputs are fairly well balanced for most compounds, a finding that suggests aerobic biodegradation may not be a key loss process in this Harbor, as has been assumed in other systems. The main pathway for inputs of all PAHs is stormwater runoff. Atmospheric deposition is an important conveyor of PAHs with molecular weights < or =202 g mol(-1). A principal objective of this report is to expose key data gaps, which include the need for comprehensive monitoring of both flow and PAH concentrations in stormwater and CSOs. An improved understanding of the key transmission routes of nonpoint source pollutants is essential for sustainable management of urban water resources.