This report mostly is a republication of a Ph.D. thesis prepared by the author for the University of California, Davis, in 1997. Only minor changes in the original thesis were made; these changes did not change the substance of the report. The reference list and the discussions of the state of knowledge in 3-D estuarine modeling have not been upgraded beyond 1997. The intent of republishing this work is to make its content available in an online format as part of the U.S. Geological Survey Open-File Report series. The version of the computer model described in this report is applicable only to simple rectangular geometries. Since 1997, it has been entirely recoded using the latest (Fortran 95) programming enhancements and generalized for applications to estuaries that have arbitrary geometries, including islands and barriers, and multiple open boundaries. The model has been used successfully in several applications to different parts of the San Francisco Bay-Delta Estuary, California. Although the model was designed mostly to apply to estuaries, the University of California, Davis, has successfully applied it to studies of lakes (Clear Lake and Lake Tahoe, California) also. Additional publications describing the model and its applications will be forthcoming.