Sturgeon populations worldwide have collapsed due to various anthropogenic impacts but knowledge gaps in habitat requirements and population dynamics still exist. In the Austrian Danube, habitat loss and the blocking of migration routes due to the construction of a chain of ten hydropower plants (HPP) had left the sterlet (Acipenser ruthenus) as the only remaining sturgeon species, which is classified as “critically endangered”. Since available estimates for the Austrian Danube were based on expert judgement, this study aims to describe the population structure and to estimate the size of a remnant sterlet population in the free-flowing section east of Vienna based on monitoring data. Net fishing was conducted over four years in the tailwater of the HPP Freudenau and population estimates were generated using Capture-Mark-Recapture techniques. A total of 38 sterlets were captured: 27 females, 7 males and 4 with unknown sex. Females were on average larger and heavier (total length (TL) = 800 ± 62 mm; weight (W) = 3294 g ± 1324 g) than males (TL = 660 ± 73 mm; W = 1350 ± 358 g). The population size was estimated at 53 individuals (95 % CI = 43–80) by the POPAN and at 48 individuals (95 % CI = 42–63) by a closed population model. These first monitoring-based population estimates in a free-flowing section of the Austrian Danube provide a base for future population monitoring and the evaluation of ongoing restocking actions. Lacking evidence of natural reproduction and a small population size pose an urgent need to restore the migration corridor and to further improve habitat quality for sturgeons in the Danube and elsewhere.