In the past, the phrase ‘environmental allocations of water’ has most often been taken to mean allocation of water to rivers. However, it is now accepted that groundwater-dependent ecosystems are an important feature of Australian landscapes and require an allocation of water to maintain their persistence in the landscape. However, moving from this theoretical realisation to the provision and implementation of a field-based management regime is extremely difficult. The following four fundamental questions are identified as being central to the effective management of groundwater-dependent ecosystems (GDEs): (1) How do we identify GDEs in the field; put another way, which species or species assemblages or habitats are reliant on a supply of groundwater for their persistence in the landscape; (2) what groundwater regime is required to ensure the persistence of a GDE; (3) how can managers of natural resources (principally water and habitats), with limited time, money and other resources, successfully manage GDEs; and (4) what measures of ecosystem function can be monitored to ensure that management is effective? This paper explicitly addresses these questions and provides a step-by-step theoretical and practical framework for providing answers. In particular, this paper provides an introduction to some of the relevant literature and from this, presents a synthesis, presented in the form of a functional methodology for managing groundwater dependent ecosystems.

Highlights d We used a transdisciplinary approach to support more inclusive water planning d We developed a hydro-socio-ecological model to underpin water allocation decisions d We propose principles for using e-flows to protect biodiversity and Indigenous values

Unprecedented growth and global expansion of human populations over the last 100 years has resulted in the widespread degradation of natural ecosystems. Of equal concern is the basic failure of people to appreciate the ecological, economic and social values of the services natural ecosystems provide and the ultimate impacts of their loss.

Riparian trees play a critical role in the ecological function of rivers, yet are threatened by anthropogenic change to the hydrological cycle. Identifying the sources of water used by riparian trees can inform sustainable water policy. We used isotopic analysis complemented by measurements of plant water relations to assess water sources for riparian trees at two sites with contrasting hydrogeological processes; one with an alluvial aquifer overlaying an aquitard, and one where fault-induced preferential pathways in the aquitard allowed the flow of deeper, older groundwater from a regional aquifer to the alluvium. At both sites, plant water potential, stomatal conductance, and plant water isotope composition in the xylem sap of riparian trees were collected from two landscape positions, the riverbank and floodplain. We used a Bayesian mixing model (MixSIAR) to assess differences in the proportion of water sources for sites and landscape positions. We found that xylem water isotope values differed between the two sites in line with their hydrogeological characteristics, with trees at the regional aquifer site using water sourced from the regional groundwater and trees at the site with only an alluvial aquifer present using a mixture of water sources, with no dominant source identified. Higher plant predawn water potential values at the regional site indicated greater water availability and support the inference that plants were using more groundwater at the regional site compared to the alluvial site. Trees closer to the river had higher isotope values, indicative of surficial water sources i.e. shallow soil water and river water. Our findings show that the water sources used by riparian trees reflect local hydrogeology and resource availability. Water managers should identify and protect plant water sources to ensure maintenance of riparian trees.

River flows are commonly altered by water resource development, with changes to the natural flow regime potentially impacting riparian vegetation. Increasingly, water resource managers seek to design policy to maintain healthy riparian ecosystems. Models that make explicit the relationship between hydrological variables and vegetation can be used by managers to assess vegetation response under different water management scenarios. We determined the potential impact of water‐takeon the spatial distribution of woody riparian plant species in the lower Fitzroy River, in north‐western Australia, an area under pressure to increase water resource development. We undertook a plant survey and developed and applied a joint species distribution model to determine the likelihood of occurrence for 26 woody riparian plant species, mapped species occurrence and assessed the change in species distribution under two water‐take scenarios. We found that the duration of inundation from flood flows was a strong predictor of species occurrence in our joint species distribution model. We identified species associated with wetter environments, as indicated by their effect size for the inundation metric. Under the 300‐Gl water‐take scenario we found little change (<2%) in species occurrence, but under the 600‐Gl scenario a decline between 5% and 7.4% was predicted for eight species associated with wetter habitats. This decline was generally confined to a localised area. Our approach highlights the usefulness of predictive modelling to identify species most likely to be impacted by water‐take, and the benefit of linking modelling to spatial mapping because it can highlight areas where change is likely to occur. This information can assist management to protect ecologically and culturally important species.