The Canterbury mudfish (Neochanna burrowsius; Galaxiidae) is a small, acutely threatened freshwater fish endemic to South Island, New Zealand, which has traits related to its historic occurrence in the wetlands of the Canterbury Plains. These wetlands have been largely transformed into productive agricultural land, with consequent fragmentation and local extinction of N burrowsius populations. N. burrowsius now persists primarily in agricultural waterways across these increasingly drought-prone plains. I examined aspects of N. burrowsius habitat, inter-specific interactions, and reproduction of importance for their conservation. Field studies focused on four sites identified as important remnant N. burrowsius habitats. These were distributed across the latitudinal range of N. burrowsius and encompassed different hydrological and agricultural disturbance regimes, and fish communities. Distributions of N. burrowsius within each site were patchy. Furthermore, the location of N. burrowsius aggregations within sites was temporally variable, and was influenced by changes in habitat quality and the presence of predatory fish. Predatory fish also affected N. burrowsius activity and abundance. At sites with intermittent flow that regularly dried up, successful strategies of drought survival were dependent on the size of N. burrowsius. Comparisons between populations indicated differences in size structure, individual growth, recruitment, deformities, disease, and parasitic infection. Experimental investigations highlighted the behavioural and physiological plasticity of N. burrowsius' responses to competition, environmental conditions during spawning, and the ability of embryos to tolerate hypoxia that likely aid survival in wetland habitats. Macrophytes were also revealed to be a key element in N. burrowsius habitat, with particular macrophyte species associated with different N. burrowsius life stages, and providing spawning substrate critical to the survival of eggs. This research indicates that hydrological disturbance and the presence of predatory fish likely had a greater effect on population characteristics than the presence of competitors, geographical location, and direct agricultural disturbance. Thus, recognising these factors will be critical in the conservation of N. burrowsius.