Successful embryonic development depends on the interaction between genetic factors and environmental variables. Congenital malformations in sea turtles can result from extreme conditions during the incubation period, reducing hatching success and potentially impeding population recovery. We aimed to characterize the congenital malformations found in green turtle nests, determine their prevalence and severity, and understand their drivers during the 2022 nesting season on Samandağ beach on northern Mediterranean nesting beaches. A total of 2986 examples of congenital malformations were observed in 362 out of 907 green turtle nests. The prevalence of congenital malformations per nest was 39%, and the severity (the number of malformed individuals per nest) was 3.8%. Nests with congenital malformations exhibited a lower mean distance from the sea, a shorter incubation duration (a proxy for incubation temperature), lower hatching success, a larger clutch size, and higher mortality at late embryonic and hatchling stages than nests without congenital malformations. There was no significant difference in total mortality between these two nest types. A total of 52 different congenital malformations were recorded, 2 of which were observed for the first time in sea turtles and 28 for the first time in green turtles. The results suggest that congenital malformations may be related to nest temperature and clutch size, while overall mortality may be independent of malformations. Pigmentation disorders and craniofacial malformations typically coexist in cases of multiple malformations. Long‐term monitoring of congenital malformations is crucial, as it can provide clues about the health status of the nesting beach and nesting colony.