Technical Abstract: Rainfall and evapotranspiration (ET) are the two major spatially distributed processes that affect hydrological responses such as surface runoff, infiltration, change in soil moisture storage, and recharge at various spatial scales. This in turn affects the quality and quantity of surface and groundwater resources. Assessing the impact of anthropogenic and naturally driven changes in water fluxes requires comprehensive modeling approaches and novel methods to measure/estimate distributed model inputs with minimum uncertainty. ET accounts for a large portion of the water budget and estimation errors can propagate non-linearly to model outputs. The Energy Balance based ET (EB_ET), Soil and Water Assessment Tool (SWAT), and the Modular Three-Dimensional Finite-Difference Groundwater Flow (MODFLOW) models are extensively used to estimate different components of the hydrological cycle but limited to the extent of each model. Therefore, none of these models can independently account the full extent of the hydrological cycle at the watershed scale. This paper presents a conceptual framework integrating five EB_ET models with SWAT and coupling SWAT with the Newton formulation for MODFLOW-2005 (MODFLOW-NWT), which was developed to improve estimation of fluxes and decrease model input uncertainty at the watershed scale. In addition, a set of new tools developed using DELPHI programming language in Windows environment to assist users to integrate the EB_ET model and create the MODFLOW project when linked with SWAT, will be presented.