This User's Guide is for the Model for Prediction Across Scales-Ocean (MPAS-Ocean), the ocean component of the Energy Exascale Earth System Model (E3SM), developed by the U.S. Department of Energy. Herein we describe the equations, namelist options, and variables for MPAS-Ocean. These settings apply to both the standalone ocean-only version of MPAS-Ocean, and E3SM version that is coupled to the atmosphere, sea ice, land ice, land and river components. The MPAS-Ocean code for both standalone and coupled is housed in the repository https://github.com/E3SM-Project/E3SM, within the directory components/mpas-ocean. The standalone executable may be built within that directory using the make command with the required libraries, as described in Chapter 1 of this guide. Documentation for the E3SM coupled climate model may be found on the E3SM docs pages, the E3SM Documentation webpage, or the E3SM repository homepage.