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Freshwater ecosystems are one of the most threatened in the world. They occupy only 0.8% of the Earth’s surface but host a third of all vertebrate species. However, the importance of freshwater for human persistence and industry mean ecosystems are threatened by extensive flow modification and water abstraction, pollution and habitat destruction. Continuation of these threats and the impact of invasive species and climate change are expected to exacerbate the rate of decline in freshwater environments. Understanding how these threats may impact species occupying freshwater environments is therefore paramount in helping preserve their existence. While much research has been conducted on fully aquatic species such as fish, less is known about semi-aquatic species that rely on both aquatic and terrestrial environments. One species whose response to changing freshwater ecosystems is largely unknown, is the rakali (Australian water rat, Hydromys chrysogaster). It is a lesser-known native rodent often under-represented in the literature, despite offering multiple ecosystem services, including top-down predation of invasive fish and facilitating nutrient exchange between aquatic and terrestrial environments. While currently considered Least Concern under the International Union for the Conservation of Nature (IUCN) Red List, its conservation status has been questioned in the literature. It has declined across Western Australia and is within the critical weight range most susceptible to predation. Further, the rakali has displayed a sensitivity to habitat changes, with local extinctions often following habitat alterations or drought events. In this thesis, I aim to 1) determine whether freshwater mammals are predisposed to a greater risk of extinction; 2) identify the most effective survey method to monitor rakali populations; 3) highlight the effectiveness of rakali in selecting invasive prey items; and 4) define habitat and hydrological characteristics important for sustaining abundant rakali populations.<br/>In chapter one, I provide an overview of the rakali and its ecology, behaviour, and history. Chapter two investigates the extinction risk of freshwater mammals globally. I show that these mammals are declining faster than other terrestrial or freshwater assemblages and identify their key threatening processes: hunting, land clearing, pollution, and water management. I considered life history traits and geographical range as predictors of extinction risk, with species in the Neotropical and Indo-Malay realms and with larger body mass and dispersal distances more likely to be threatened.<br/>Most studies of rakali rely on cage trapping, however trap rates are highly varied, making the species difficult to study. In chapter three, I compare the effectiveness of three main detection methods—visual surveys, live cage trapping and camera trapping—and their placement next to and within a waterbody. Camera traps have had mixed success with detecting semi-aquatic mammals thus, three camera angles were also tested: forward-facing, downward-facing and overlooking a floating platform. Cameras and traps placed in the water outperformed those on land. Nightly visual surveys were the most efficient method, followed by platform facing cameras. I show that passive infrared cameras can detect rakali even when they are wet, which has been identified as a limitation of this method for other semi-aquatic species.<br/>Chapter four presents a research note on rakali diet. Previous research on the rakali diet was conducted over 45 years ago through morphological analysis, where they were reported to prefer invasive species. I collected scat samples during camera trap surveys to identify the diet of the rakali with robust DNA metabarcoding analysis. I confirmed that the rakali diet is comprised mostly of invasive species, such as the European carp (Cyprinus carpio) and mosquitofish (Gambusia spp.), and highlight an unexpectedly high proportion of plant matter consumed.<br/>In chapter five, I modelled the abundance of rakali collected through extensive camera trapping surveys, to determine key habitat and hydrological factors that affect rakali populations. This was measured at site and landscape levels with satellite derived water and vegetation metrics. The type of habitat was important, with greater abundance of rakali present in creeks and riparian billabongs compared to swamps, lakes or irrigation channels. Rakali abundance increased with the proportion of green vegetation and the level of water permanence in creek habitats. I found greater rakali abundance in areas with moderate to steep bank slopes and, unexpectedly, in low oxygenated waters.<br/>Collectively, the findings in this thesis expand on the known ecology of the rakali and highlight the importance of preserving a member of a highly threatened and unique group of mammals. I provide a novel method in which to monitor the species with applications that extend internationally to other semi-aquatic species. I demonstrate the population level and behavioural responses of rakali to various habitat and hydrological factors and stress the importance of sustaining permanent water refuges and surrounding vegetation for rakali persistence in adverse conditions. I also showcase the rakali as an important top predator of invasive fish species, particularly carp, which have contributed to worsening the water quality of inland waterways.