In environments with shallow ground water elevation, small changes in the water table can cause significant variations in recharge and evapotranspiration fluxes. Particularly, where ground water is close to the soil surface, both recharge and evapotranspiration are regulated by a thin unsaturated zone and, for accuracy, must be represented using nonconstant and often nonlinear relationships. The most commonly used ground water flow model today, MODFLOW, was originally designed with a modular structure with independent packages representing recharge and evaporation processes. Systems with shallow ground water, however, may be better represented using either a recharge function that varies with ground water depth or a continuous recharge and evapotranspiration function that is dependent on depth to water table. In situations where the boundaries between recharging and nonrecharging cells change with time, such as near a seepage zone, a continuous ground water flux relationship allows recharge rates to change with depth rather than having to calculate them at each stress period. This research article describes the modification of the MODFLOW 2000 recharge and segmented evapotranspiration packages into a continuous recharge-discharge function that allows ground water flux to be represented as a continuous process, dependent on head. The modifications were then used to model long-term recharge and evapotranspiration processes on a saline, semiarid floodplain in order to understand spatial patterns of salinization, and an overview of this process is given.