In the summer and autumn of 2015, the Bellinger River snapping turtle (Myuchelys georgesi), a narrow‐range endemic of eastern New South Wales, Australia, suffered mass mortality from epidemic disease, apparently caused by a previously unknown virus. Information on the current population size and structure of M. georgesi, and the body condition and growth of the surviving individuals, is needed to support planning of conservation actions. Population estimates are also needed for a sympatric population of the widely distributed Macquarie turtle (Emydura macquarii), which has probably been introduced to the Bellinger River and may threaten the persistence of M. georgesi through hybridization, competition, and disease transmission. Data from five turtle surveys between November 2015 and November 2018 were used to estimate populations of the two species in the Bellinger River by an analysis based on habitat extent and turtle detectability. Changes in the body condition of M. georgesi and the body growth of both species were also assessed. Current populations of ~150 M. georgesi and ~500 E. macquarii are indicated, although the uncertainty of these estimates is high. The estimate for M. georgesi represents a decline of >90% from the historical population. Moreover, about 88% of the surviving M. georgesi are immature, and only about 5% are mature females. However, the body condition of the survivors has improved recently. Growth models suggest that M. georgesi matures later than E. macquarii, which may provide the latter with a competitive advantage. Evidence presented here does not support a previous hypothesis that M. georgesi were predisposed to disease through malnutrition and consequently reduced immune competence caused by high water temperatures and low river flows. Continuing disease, hybridization, and interspecific competition are probably the greatest threats to the persistence of the species.