The development of computer models for mass transport in estuaries has been an important engineering activity for the past decade. However, only a limited amount of work has been done in modeling the two-dimensional characteristics of partially stratified estuaries. Explicit and Crank-Nicolson finite difference models were developed for the one- and two-dimensional estuary equations with varying coefficients. The concentration profiles for instantaneous releases and for steady-state conditions were analyzed. Accuracy was determined by comparison with analytical closed-form solutions. Models were developed also to analyze the profiles for biochemical oxygen demand and dissolved oxygen under time-changing conditions, for both aerobic and anaerobic conditions. Applicability of these models to partially stratified estuaries was established by comparisons with dye study data from the Houston Ship Channel. (Author Modified Abstract)