Population structure, age, growth, mortality, and reproduction patterns of the Mediterranean green crab Carcinus aestuarii were determined for the native population in Parila Lagoon (Neretva Estuary, Middle Adriatic, Croatia). The population size structure showed two distinct cohorts: (1) specimens with a carapace width of 20–34 mm and dominated by females and (2) large‐sized specimens with a carapace width > 34 mm with males significantly dominating and no females found above 46 mm. Males appeared to grow faster than females in the first and second year of the life cycle. Most of the natural mortality (70.4%) occurred during the first year of life. This indicates high predation pressure from fish and other crab species on small‐sized (less than 25 mm) C. aestuarii cohorts. The peak of ovigerous female occurrence occurred in January 2015. A very small percentage of ovigerous females appeared in June 2015. The 50% ovigerous size for the population was estimated at a carapace width of 29.65 mm and weight of 10.39 g. The average fecundity was 61,017 eggs/female, with an average fecundity per gram of female wet weight of 4,804 eggs. The biological characteristics and population dynamics of C. aestuarii show that life history traits of this species (such as the smallest and average ovigerous female size, the mortality rate during the first year of life or the establishment of a second year, and a late‐spring reproduction period) should be used to monitor potential changes in ecosystem properties of Mediterranean transitional waters and to manage potential fisheries.