Irrigation is an important activity on many dry tropical coastal floodplains in northern Australia. Lack of understanding of floodplain dynamics and its role as a source or sink of solutes (salts, nutrients, agrochemicals) is causing concern about the long term sustainability of current management practices. Issues include salinity associated with rising water tables, deteriorating surface and groundwater quality, and threats of seawater intrusion in coastal areas that rely on bores for irrigation water. Addressing these issues requires improved understanding of the geochemistry of the groundwater systems and adoption of a systems approach to better understand and manage the links between land management practices and surrounding water systems. This paper outlines key biophysical processes involved and various project activities being undertaken at a range of scales to improve understanding of floodplain dynamics and the impacts of current management practices on water quality. Emerging understanding indicates opportunities for both economic and environmental gains.