Estuaries in urban regions present unique environmental management challenges. Ecosystems in urban estuaries are typically impacted by habitat loss and degradation, watershed modification, and nonpoint and point sources of many chemicals. Restoring such systems requires an understanding of the relative contribution of various stressors to overall ecological conditions and an understanding of shifting patterns of stress over time. In this article, we present the results of a multiparameter environmental assessment of a quintessential urbanized waterway: the lower Passaic River in the vicinity of Newark, New Jersey, USA. To provide the foundation for effective management decision making, we quantified baseline conditions (habitat losses and degradation), chemical concentrations in sediment and biota relative to published toxic effect levels, direct toxicity of sediments to benthic organisms, and food-web mediated risks to fish-eating birds. Habitat losses have been severe (greater than 85% of wetlands, nearly 100% of the total length of tidal and nontidal tributaries, and 100% of natural shoreline habitat have been lost), resulting in substantial habitat constraints on biota. Despite this, biological communities are present in the lower Passaic. In general, concentrations of toxic chemicals in surface sediments have fallen with time, and natural recovery processes are proceeding. Chemical concentrations remain high enough to impair survival of amphipods, but not amphipod growth or polychaete growth or survival as measured in laboratory bioassays using field-collected sediment. Fish and blue crab body burdens of some metals, PCBs, and the pesticide, DDT, are at concentrations sufficiently high to exceed toxicity thresholds. The resident fish-eating bird--the belted kingfisher--is at exposure risk from some metals, PCBs, and polychlorinated dibenzo-p-dioxins and dibenzo furans (PCDD/Fs). Migratory waders--the herons and egrets--are not at risk from chemical exposure. These complex findings suggest that restoring the lower Passaic River to ecological health is a correspondingly complex task. Habitat constraints must be eased for biotic components of the ecosystem, and chemical effects must be reduced for those organisms that are present. Only a coordinated, multidisciplinary restoration program will succeed in this challenging environment.