The following instructional text is an overview of the tidally- and cross-section-averaged finite element Water Analysis Module (WAM). The model was developed by the Resource Management Associates, Inc. (RMA) as part of the first phase of the Delta Risk Management Strategy (DRMS) program. The document is presented as a set of instructions from which users can design their own modeling scenarios for the Sacramento-San Joaquin Delta in WAM. Since no graphical interface currently exists for the program, it discusses operation of the model based on manipulation of the many files required for running various parts of the model. The manual does not provide an extensive overview of the model logic and physics, although links to website-hosted documents with information about WAM are provided throughout the text. Emphasis is placed in describing the submodels and control files within WAM, which are collectively responsible for controlling water operations, net delta area losses of water (NDAL), hydrodynamics and water quality (HD), and the breach sequence of flooding islands. The inputs defined within these files are discussed in detail. Additionally, the manual provides an example for changing WAM from one modeling scenario to another, and describes utilities available to display and process output data from the model results. Much of the information provided within the many files that are required for WAM to function is derived from extensive research or calibration. The user must exercise caution in making edits to files that control important model aspects. Information such as reservoir operations logic or dispersion coefficients should not be changed without contacting the persons who developed these parts of the model, to ensure a proper understanding of the relevant parameters. The manual provides information about all of the files necessary for performing simulations with WAM and how they can be edited, so that the user can gain insight into their respective roles.