Water mass transformation theory provides conceptual tools that in principle enable innovative analyses of numerical ocean models; in practice, however, these methods can be challenging to implement and interpret, and therefore remain under-utilized. Most prior work evaluates only some of the simpler or more accessible terms in the water mass budget; meanwhile, the few full budget calculations in the literature are either limited to idealized model configurations and geometrically-simple domains or else have required heroic efforts that are neither scalable to large data sets nor portable to other ocean models or research questions. We begin with a pedagogical derivation of key results of classical water mass transformation theory. We then describe best practices for diagnosing each of the water mass budget terms from the output of Finite-Volume Generalized Vertical Coordinate (FV-GVC) ocean models, including the identification of a non-negligible remainder term as the spurious numerical mixing due to advection scheme discretization errors. We illustrate key aspects of the methodology through an example application to diagnostics from a polygonal region of a Baltic Sea regional configuration of the Modular Ocean Model v6 (MOM6). We verify the convergence of our WMT diagnostics by brute-force, comparing time-averaged diagnostics on various vertical grids to timestep-averaged diagnostics on the native model grid. Finally, we briefly describe a stack of xarray-enabled Python packages for evaluating WMT budgets in FV-GVC models, which is intended to be model-agnostic and available for community use and development.