AbstractCooper Creek is one of Australia's largest unregulated river systems and one of the world's most variable large river systems. It is a dynamic environment that oscillates between booms and busts; yet, many species thrive in it. One of these species, the Cooper Creek turtle (Emydura macquarii emmotti) has received little attention, despite being one of Australia's largest freshwater turtles and living further inland than any other Australian turtle. We conducted surveys for E. m. emmotti in 2001–2004, 2019, and 2022, focussing predominantly on the Waterloo waterhole. Waterloo had a large population of E. m. emmotti (508 estimated individuals; 95% CI = 447–596) with an estimated density of 64.8 turtles/ha (95% CI = 57.0–76.2) and estimate biomass of 74.4 kg/ha (95% CI = 57.6–100.3 kg/ha). Juveniles were highly abundant in all years, representing up to 63.6% of captured individuals. It was slightly (but not significantly) male‐biased in 2001–2004 and significantly female‐biased in 2019. All sizes and sexes used the floodplain during a flooding event in 2022, but more males than females were captured on the floodplain, and there was evidence of male‐biased dispersal across the years. Compared to Murray River turtles (Emydura macquarii macquarii), E. m. emmotti exhibited megacephaly across all ages and sexes, with particularly pronounced megacephaly in adult females. Algae were present on many individuals (including on the skin and plastron) but was relatively more abundant on juveniles. Leeches were not detected on any of the 66 turtles that were examined for them. The following injuries/malformations were noted: missing or injured limbs (3.2%), missing or injured eyes (1.3%), damaged shells (8.0%), scute/shell anomalies and malformations (10.6%), and marginal scute seams extending into the costals (67.4% of adults, 1.2% of juveniles). This paper presents some of the first work on this unusual turtle and makes recommendations for future research.