Freshwater ecosystems are one of the most endangered systems in the world, and consequently many inhabitants also face a higher risk of extinction. Comparatively, little research has been conducted on semi-aquatic mammals that rely on both freshwater and terrestrial ecosystems. A review was conducted on the extinction risk of aquatic and semi-aquatic freshwater mammals globally. Patterns in location, threats and biological traits that predispose species to a greater risk of endangerment were identified. Freshwater mammals had a higher risk of extinction and are declining more rapidly than total freshwater and mammal species respectively. Hunting, land clearing, pollution and habitat modification posed the greatest threats to these species, particularly from agricultural practices and residential development. Many species remained poorly known and lacked basic life history knowledge indicating more research is needed for this group. To begin expanding on this, camera traps were used to explore the habitat and hydrological preferences of the understudied native rakali (Hydromys chrysogaster). Local and landscape-level variables were investigated with on site data and the remote sensing Wetlands Insights Tool which provided long term temporal and spatial data. Habitat relationships were scale dependent with landscape level vegetation and wetland type displaying the greatest effects. Local-scale habitat characteristics such as dissolved oxygen, flow rate, number of nesting logs, red fox (Vulpes vulpes) presence and bank slope also influenced rakali abundance. Rakali are most abundant in lotic systems with higher water permanence, moderate bank slope and high vegetation cover. We highlight the importance of environmental flows in maintaining permanent streams and refuge habitat and recommend land managers adopt riparian revegetation projects to provide refuge from predators and maintain good bank stability.