Former commercial salt ponds in Alviso, California, now are operated by the U.S. Fish and Wildlife Service (USFWS) to provide habitat for birds. The USFWS has modified the operation of the ponds to prevent exceedingly high salinity. Ponds that were formerly hydraulically isolated from South San Francisco Bay and adjacent sloughs now are managed as flow-through ponds, and some are allowed to discharge to the Bay and sloughs. This discharge is allowed under a permit issued by the Regional Water Quality Control Board. As a requirement of the permit, the USFWS must estimate the amount of discharge from each discharge pond for the period May through November of each year. To facilitate the accurate estimation of pond discharge, a calculation methodology (hereafter referred to as 'calculator' or PONDCALC) for the discharging Alviso ponds has been developed as a Microsoft Excel file and is presented in this report. The presence of flap gates on one end of the discharge culverts, which allow only outflow from a pond, complicates the hydraulic analysis of flow through the culverts. The equation typically used for culvert flow contains an energy loss coefficient that had to be determined empirically using measured water discharge and head at the discharge structure of one of the ponds. A standard weir-flow equation is included in PONDCALC for discharge calculation in the ponds having weir box structures in addition to culverts. The resulting methodology is applicable only to the five Alviso ponds (A2W, A3W, A7, A14, and A16) that discharge to South San Francisco Bay or adjacent sloughs under the management practices for 2005.