Operating on the basic principle of water balance accounting, WEAP is applicable to municipal and agricultural systems, single subbasins or complex river systems. Moreover, WEAP can address a wide range of issues, e.g., sectoral demand analyses, water conservation, water rights and allocation priorities, groundwater and streamflow simulations, reservoir operations, hydropower generation and energy demands, pollution tracking, ecosystem requirements, and project benefit-cost analyses.

The analyst represents the system in terms of its various supply sources (e.g., rivers, creeks, groundwater, reservoirs); withdrawal, transmission and wastewater treatment facilities; ecosystem requirements, water demands and pollution generation. The data structure and level of detail may be easily customized to meet the requirements of a particular analysis, and to reflect the limits imposed by restricted data.

WEAP applications generally include several steps. The study definition sets up the time frame, spatial boundary, system components and configuration of the problem. The Current Accounts provide a snapshot of actual water demand, pollution loads, resources and supplies for the system. Alternative sets of future assumptions are based on policies, costs, technological development and other factors that affect demand, pollution, supply and hydrology. Scenarios are constructed consisting of alternative sets of assumptions or policies. Finally, the scenarios are evaluated with regard to water sufficiency, costs and benefits, compatibility with environmental targets, and sensitivity to uncertainty in key variables.