The European project Nature-SDIplus has developed data and metadata specifications for three INSPIRE Annex III themes: Habitat and Biotopes, Bio-geographical regions and Species distributions. These serves as a foundation for the thematic groups developing the corresponding INSPIRE specifications. The aim of this study is to test a data harmonization approach to make Swedish environmental geodata and metadata compliant with these specifications. In the harmonization process, we use offline transformations that are split into one spatial and one non-spatial part, and standardized formats to allow vendor neutrality. Moreover, we extend the compliance tests to the data and metadata specifications by validating against both extensible Markup Language (XML)-schema and Schematron. Finally, we identify harmonization processes that may be costly or have negative impacts on data quality. The harmonized data and metadata are thereafter published as network services compliant with OGC Web Service specifications. The output from our method is data and metadata that are valid to the Nature-SDIplus data specifications and metadata profiles. Although the usage of standardized formats facilitates vendor neutrality, the nonspatial transformation procedures expressed in interoperable languages seem to be insufficient to execute all the mapping rules. Therefore, some of these transformations cannot be executed in a vendor neutral environment without modifications. Furthermore, by splitting the harmonization into two manageable parts, we avoid some limitations about XML schema translations in existing spatial transformation tools. Additional findings are: (1) by extending the validation with Schematron tests, we find non-compliances that have been missed during the XML schema tests; (2) costly processes are identified, which are caused by missing elements and by unstructured information given as comments; and (3) degradation of the positional and thematic accuracy occur during the harmonization.