Linear alkylbenzenes (LABs) were used to assess the fates of hydrophobic organic compounds (HOCs) released to a large urban harbor and the adjoining offshore waters. We found that particulate concentrations of the individual C12 LAB isomers in 1996 summertime surface waters decreased from 1 pM in Boston Harbor to 20-200 fM in coastal Massachusetts and Cape Cod Bays. Levels fell to only a few fM in offshore Gulf of Maine locations. These observations were consistent with municipal wastewater in Boston Harbor as the predominant input followed by dispersal via known circulation patterns in this region. Phase-dependent removal rate coefficients for flushing, vertical scavenging, volatilization, photodegradation, and biodegradation of individual LAB isomers were constrained from literature, field observations, and laboratory experiments and combined with estimates of wastewater release rates into a predictive 3-box model. Vertical scavenging, biodegradation, and flushing were predicted to be the most important fate processes for C12 LABs in the Boston Harbor-MA Bay-Cape Cod Bay flow system with about 1% of the harbor releases "surviving" passage. For HOCs such as the relatively bio-recalcitrant LAB, 6-phenyldodecane, it appears that we are at present able to predict the coastal fate of harbor-introduced HOCs in this system within a factor of 2. Contrary to expectations from biodegradation experiments, the ratio of internal-to-external (I/E) LAB isomers decreased offshore in both water and sediment samples, suggesting we are "missing" an important process affecting LAB fates.