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Reference ontologies are intended to aid domain ontology design, identify gaps and inconsistencies in representations of domain information, and facilitate data interoperability. The application of a reference ontology to the water domain is untested. We present findings from using a first-order logic reference ontology for the water domain, the Hydro Foundational Ontology (HyFO), to identify and remedy semantic gaps and inconsistencies in the Groundwater Markup Language (GWML2), a data model for groundwater information with less detailed formal semantics. We express GWML2 as a logical extension of HyFO, thereby improving GWML2's compatibility with other hydro data models. We derive general desiderata for a "good" domain reference ontology in the geosciences and discuss the benefits one can expect from their use for the ontological analysis of geoscience data models.

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