A national approach to the conservation of biodiversity in Australia's freshwater ecosystems is a high priority. This requires a consistent and comprehensive system for the classification, inventory, and assessment of wetland ecosystems. This paper, using the State of Victoria as a case study, compares two classification systems that are commonly utilized to delineate and map wetlands--one based on hydrology (Victorian Wetland Database [VWD]) and one based on indigenous vegetation types and other natural features (Ecological Vegetation Classes [EVC]). We evaluated the extent of EVC mapping of wetlands relative to the VWD classification system using a number of datasets within a geographical information system. There were significant differences in the coverage of extant EVCs across bioregions, different-sized wetlands, and VWD wetland types. Resultant depletion levels were markedly different when examined using the two systems, with depletion levels, and therefore perceived conservation status, of EVCs being significantly higher. Although there is little doubt that many wetland ecosystems in Victoria are in fact threatened, the extent of this threat cannot accurately be determined by relying on the EVC mapping as it currently stands. The study highlighted the significant impact wetland classification methods have in determining the conservation status of freshwater ecosystems.