ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, MT3D-USGS, and WellFootprint and the non-USGS model MT3DMS. This software package provides a GUI for creating the flow and transport input file for PHAST and the input files for the other models. In ModelMuse, the spatial data for the model are independent of the grid, and the temporal data are independent of the stress periods. Being able to input these data independently allows the user to redefine the spatial and temporal discretization at will. This report describes the basic concepts required to work with ModelMuse. These basic concepts include the model grid, data sets, formulas, objects, the method used to assign values to data sets, and model features. The ModelMuse main window has a top, front, and side view of the model that can be used for editing the model, and a 3–D view of the model that can be used to display properties of the model. The side view is hidden for SUTRA models. Only the top view is visible for WellFootprint projects. ModelMuse has tools to generate and edit the model grid. It also has a variety of interpolation methods and geographic functions that can be used to help define the spatial variability of the model. ModelMuse can be used to execute the models and can also display the results of all the models except PHAST and ZONEBUDGET. An example of using ModelMuse with MODFLOW–2005 is included in the report. Several additional examples are described in the help system for ModelMuse, which can be accessed from the Help menu. This report (1) describes modifications to ModelMuse,as described in U.S. Geological Survey (USGS) Techniques and Methods (TM) 6–A29 (Winston, 2009), to add support for the Saturated-Unsaturated Transport model (SUTRA) (Voss and Provost, 2002; version of September 22, 2010) and (2) supplements USGS TM 6–A29. Modifications include changes to the main ModelMuse window where the model is designed, addition of methods for generating a finite-element mesh suitable for SUTRA, defining how some functions should apply when using a finite-element mesh rather than a finite-difference grid (as originally programmed in ModelMuse), and applying spatial interpolation to angles. In addition, the report describes ways of handling objects on the front view of the model and displaying data. A tabulation contains a summary of the new or modified dialog boxes. ModelMuse, a graphical user interface for groundwater-modeling software, was modified to support MODFLOW 6. ModelMuse works with two types of spatial discretization in MODFLOW 6: structured grids (DIS) and discretization by vertices (DISV). Quadtree refinement is used to generate a DISV model from a structured-grid model. The locations and weights for ghost nodes used to improve DISV model accuracy are computed automatically by ModelMuse using a new algorithm. ModelMuse does not support other types of DISV grids and unstructured grids. ModelMuse supports options in MODFLOW 6 that designate individual cells as confined or convertible and remove inactive cells associated with discontinuous layers, thereby reducing the computational burden. ModelMuse can specify fully three-dimensional (3D), spatially variable anisotropy in hydraulic conductivity. Although MODFLOW 6 does not support the parameters supported by MODFLOW–2005, ModelMuse provides backward compatibility by allowing ModelMuse parameters to specify scale-factor variables in MODFLOW 6 time-series files within packages that support time-series files. ModelMuse can automatically convert the data for many of the packages from other MODFLOW models to the new data for these packages in MODFLOW 6. Some packages, such as the Streamflow Routing (SFR) package, changed significantly enough that only a partial conversion is possible. Head and flow observations in older models are also converted to observation locations in the MODFLOW 6 Observation Utility. ModelMuse accommodates the ability of MODFLOW 6 to store specific discharge components by allowing the user to visualize the components of a specific discharge on the model grid. ModelMuse supports the versions of MODPATH and ZONEBUDGET compatible with MODFLOW 6.