The northern tropical river and wetland systems of Australia cover a vast and mostly remote area. Comparably little is known of wetland type, species diversity, ecological processes and ecosystem services. Systematic inventory and classification is lacking and research remains disparate in purpose and coverage. An integrated framework is used to evaluate results from three multidisciplinary studies across various scales to synthesise available knowledge relating to key ecological attributes across both the study region and within focus areas. The utility of geomorphic and hydrological classification at coarse scales is supported but the unavailability of biological data at corresponding and finer spatial and temporal scales constrains the potential for ecological inventory and classification utilising existing information.Future inventory and ecological studies across this and similar vast study areas need to consider the apriori development of a user-driven data framework and the development of specific investigatory tools to overcome technical and other barriers associated with the requirements of multi-scalar ecological studies.