Riparian trees are critically important for maintaining the ecological function of freshwater ecosystems. Globally, anthropogenic changes to water regimes are impacting the health and distribution of riparian trees. Water resource managers seeking to develop policy that mitigates impacts on riparian vegetation require ecological information on the water requirements of riparian vegetation. However, for many ecosystems, detailed flow-ecology data are not available. This is particularly the case in remote areas, such as the ecologically and culturally significant Fitzroy River in north-western Australia. In response to increased pressure for water development of the system, we collaborated with water managers to complete a series of studies to improve hydro-ecological knowledge to inform water management policy, with the aim to conserve the ecological values of the system. We used regional and international research to underpin a hydro-ecological-social (HSE) conceptual model and a set of key considerations for water planners. The review highlighted the paucity of data for riparian vegetation in the region, with very limited hydro-ecological evidence to draw upon to inform management decisions. Subsequent field-based research focussed on key knowledge gaps, investigating the relationship between the distribution and structure of riparian tree species and surface water flows, the use of different groundwater sources in the dry season, and the values of key functional traits for dominant tree species. The new knowledge gained through the research program was incorporated into a revised hydro-ecological model populated with data specific to the lower Fitzroy River. The studies completed as part of this project will directly informed the environmental water considerations in water planning for the Fitzroy River with the aim of conserving riparian vegetation in this data-limited, remote environment.