This report describes Phase II modifications made to the Water Availability Tool for Environmental Resources (WATER), which applies the process-based TOPMODEL approach to simulate or predict stream discharge in surface basins in the Commonwealth of Kentucky. The previous (Phase I) version of WATER did not provide a means of identifying sinkhole catchments or accounting for the effects of karst (internal) drainage in a TOPMODEL-simulated basin. In the Phase II version of WATER, sinkhole catchments are automatically identified and delineated as internally drained subbasins, and a modified TOPMODEL approach (called the sinkhole drainage process, or SDP-TOPMODEL) is applied that calculates mean daily discharges for the basin based on summed area-weighted contributions from sinkhole drain-age (SD) areas and non-karstic topographically drained (TD) areas. Results obtained using the SDP-TOPMODEL approach were evaluated for 12 karst test basins located in each of the major karst terrains in Kentucky. Visual comparison of simulated hydrographs and flow-duration curves, along with statistical measures applied to the simulated discharge data (bias, correlation, root mean square error, and Nash-Sutcliffe efficiency coefficients), indicate that the SDPOPMODEL approach provides acceptably accurate estimates of discharge for most flow conditions and typically provides more accurate simulation of stream discharge in karstic basins compared to the standard TOPMODEL approach. Additional programming modifications made to the Phase II version of WATER included implementation of a point-and-click graphical user interface (GUI), which fully automates the delineation of simulation-basin boundaries and improves the speed of input-data processing. The Phase II version of WATER enables the user to select a pour point anywhere on a stream reach of interest, and the program will automatically delineate all upstream areas that contribute drainage to that point. This capability enables automatic delineation of a simulation basin of any size (area) and having any level of stream-network complexity. WATER then automatically identifies the presence of sinkholes catchments within the simulation basin boundaries; extracts and compiles the necessary climatic, topographic, and basin characteristics datasets; and runs the SDP-TOPMODEL approach to estimate daily mean discharges (streamflow).