Abstract: Globally, the value of integrating multiple knowledge systems is being recognised in ecosystem assessments, monitoring and management. This paper describes a participatory eco-cultural assessment of freshwater billabongs in the South East Arnhem Land Indigenous Protected Area, northern Australia, that drew on Indigenous ecological knowledge (IEK) and Western science using social and natural science research methods. IEK holders were concerned about feral ungulates trampling and consuming traditional bush food resources and reducing water quality, affecting eco-cultural values of billabongs. We recorded qualitative IEK and conducted a multivariate snapshot assessment of billabong physiochemical water quality, ground condition, yarlbun (water lily) cover and macroinvertebrate assemblage that showed distinct seasonal variation. Although both knowledge systems revealed indicators of seasonal change over 1 year, IEK also revealed longer-term changes and that degradation of billabongs in the late dry season was exacerbated by feral ungulates. This participatory research illustrates how the condition of freshwater systems can be assessed using cross-cultural techniques, how these techniques can reveal more nuanced understandings of eco-cultural condition and the value of including IEK for setting ecological baselines and recording long-term change.