The recent decades have seen a shift in the management paradigm towards a healthy, working Murray-Darling Basin. While environmental management recognises the importance of ecosystem functions, to date there has been limited understanding of the underlying processes and interactions, or ecosystem functions at a basin scale, and the essential role they play in healthy water-dependent ecosystems. Identifying key ecosystem functions that can be managed at a basin scale remains a challenge, stemming from limited continuous ecological data and difficulties in reliably scaling the processes to represent spatial and temporal patterns. Remotely sensed geospatial and biodiversity data along with novel data merging and modelling techniques have the potential to address some limitations/gaps and provide deeper understanding of ecosystem responses at basin scale. In this talk, we present recent advances in understanding selected ecosystem functions through the lens of connectivity in the Murray-Darling Basin. We highlight the challenges and outline criteria to select ecosystem functions and showcase new ways of integrating data and modelling to address knowledge gaps.