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This document describes a computer program that simulates three-dimensional groundwater systems using the finite-element method. The program was developed to simulate regional groundwater systems, but it can be applied to small-scale problems as well. This program can be used to simulate both confined and water-table aquifers. The program simulates a linearized three-dimensional free-surface groundwater system with a fixed grid. FEMFLOW3D is applicable to the simulation of various free-surface groundwater systems for which the change in aquifer thickness is small relative to the overall aquifer thickness. The finite-element method provides flexibility in the design of a geometric grid that represents the physical dimensions of an aquifer system. For example, features that can be well represented with a finite-element grid include irregular, random geographic and geologic features; irregular boundaries; and increased detail within localized areas of particular interest within the study area. The structure of the computer program consists of a main program, which serves as a simple driver, and a set of subroutines in which the calculations are performed. The background, mathematical basis, structure, and inputs for each of the subroutines are described in the document where applicable. Each subroutine generally handles (1) a part of the mathematical calculations related to the finite-element method, (2) a specific feature of the hydrologic system, or (3) special features related to the management input or output data. Hydrologic features that can be represented with the program include stream-aquifer interactions, phreatophytic evapotranspiration, highly permeable fault zones, land subsidence, and land-aquifer interactions associated with land-use activities. The program can also represent the primary features associated with complex irrigation systems, such as irrigated agriculture, and can calculate the groundwater recharge that results from these activities. Three boundary conditions, including specified-head boundaries, specified-flux boundaries, and variable-flux boundaries, can be represented with the program. The program also provides a method for identifying aquifer and riverbed parameters that can be used in the calibration of models.