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.