This report describes the results from the 1996 Regional Monitoring Program for Trace Substances (RMP). It is the fourth Annual Report from the RMP which began in 1993 and attempts to synthesize the most obvious data patterns from the last four years. This report includes data from Base Program monitoring activities, as well as results of Pilot and Special Studies conducted or completed in 1996. Additionally, several articles contributed by RMP investigators and others, are included. These articles provide perspective and insight on important contaminant issues identified by the RMP. This summary addresses which kinds of pollutants measured by the RMP appear to be at levels that warrant concern, what kinds of trends may be discerned, and which stations have consistently shown elevated contaminant levels. The goals or general objectives of the RMP are: 1. To obtain high quality baseline data describing the concentrations of toxic and potentially toxic trace elements and organic contaminants in the water and sediment of the San Francisco Estuary. 2. To determine seasonal and annual trends in chemical and biological water quality in the San Francisco Estuary. 3. To continue to develop a data set that can be used to determine long-term trends in the concentrations of toxic and potentially toxic trace elements and organic contaminants in the water and sediments of the San Francisco Estuary. 4. To determine whether water quality and sediment quality in the Estuary at large are in compliance with objectives established by the Basin Plan (the regulatory planning document used by the Regional Water Quality Control Board). 5. To provide a database on water and sediment quality in the Estuary which is compatible with data being developed in other ongoing studies, including wasteload allocation studies and model development, sediment quality objectives development, in-bay studies of dredged material disposal, Interagency Ecological Program (IEP) water quality studies, primary productivity studies, local effects biomonitoring programs, and state and federal mussel watch programs.