The ability to dynamically simulate the integrated supply-and-demand components of irrigated agricultural is needed to thoroughly understand the interrelation between surface water and groundwater flow in areas where the water-use by vegetation is an important component of the water budget. To meet this need, the computer program Farm Process (FMP1) was updated and refined for use with the U.S. Geological Survey's MODFLOW-2005 groundwater-flow model, and is referred to as MF2005-FMP2. The updated program allows the simulation, analysis, and management of nearly all components of human and natural water use. MF2005-FMP2 represents a complete hydrologic model that fully links the movement and use of groundwater, surface water, and imported water for water consumption of irrigated agriculture, but also of urban use, and of natural vegetation. Supply and demand components of water use are analyzed under demand-driven and supply-constrained conditions. From large- to small-scale settings, the MF2005-FMP2 has the unique set of capabilities to simulate and analyze historical, present, and future conditions. MF2005-FMP2 facilitates the analysis of agricultural water use where little data is available for pumpage, land use, or agricultural information. The features presented in this new version of FMP2 along with the linkages to the Streamflow Routing (SFR), Multi-Node Well (MNW), and Unsaturated Zone Flow (UZF) Packages prevents mass loss to an open system and helps to account for 'all of the water everywhere and all of the time'. The first version, FMP1 for MODFLOW-2000, is limited to (a) transpiration uptake from unsaturated root zones, (b) on-farm efficiency defined solely by farm and not by crop type, (c) a simulation of water use and returnflows related only to irrigated agriculture and not also to non-irrigated vegetation, (d) a definition of consumptive use as potential crop evapotranspiration, (e) percolation being instantly recharged to the uppermost active aquifer, (f) automatic routing of returnflow from runoff either to reaches of tributary stream segments adjacent to a farm or to one reach nearest to the farm's lowest elevation, (g) farm-well pumping from cell locations regardless of whether an irrigation requirement from these cells exists or not, and (h) specified non-routed water transfers from an undefined source outside the model domain. All of these limitations are overcome in MF2005-FMP2. The new features include (a) simulation of transpiration uptake from variably saturated, fully saturated, or ponded root zones (for example, for crops like rice or riparian vegetation), (b) definition of on-farm efficiency not only by farm but also by crop, (c) simulation of water use and returnflow from non-irrigated vegetation (for example, rain-fed agriculture or native vegetation), (d) use of crop coefficients and reference evapotranspiration, (e) simulation of the delay between percolation from farms through the unsaturated zone and recharge into the uppermost active aquifer by linking FMP2 to the UZF Package, (f) an option to manually control the routing of returnflow from farm runoff to streams, (g) an option to limit pumping to wells located only in cells where an irrigation requirement exists, and (h) simulation of water transfers to farms from a series of well fields (for example, recovery well field of an aquifer-storage-and-recovery system, ASR). In addition to the output of an economic budget for each farm between irrigation demand and supply ('Farm Demand and Supply Budget' in FMP1), a new output option called 'Farm Budget' was created for FMP2, which allows the user to track all physical flows into and out of a water accounting unit at all times. Such a unit can represent individual farms, farming districts, natural areas, or urban areas. The example model demonstrates the application of MF2005-FMP2 with delayed recharge through an unsaturated zone, rejected infiltration in a riparian area, changes in de