This paper presents a methodology that can be used for determining the optimal freshwater inflows into bays and estuaries for the purpose of balancing freshwater demands with the harvest of various types of estaurine resource. Salinity is expressed as a function of freshwater inflow in a nonlinear regression equation and used as a constraint. Additional nonlinear constraints are the harvest regression equations for the various species which express harvest as a function of the quantity of freshwater inflow. Because of the uncertainty associated with the regression equations for salinity and harvest these constraints are expressed in a chance-constrained formulation. The methodology has been applied to the Lavaca-Tres Palacios Estuary in Texas.