In the third edition of The Princeton Field Guide to Dinosaurs, Gregory S. Paul stated its length at 0.7 metres (2.3 ft) and weight at 0.3 kilograms (0.66 lb).

[4] Natovenator is different from other halszkaraptorines due to features such as a wide groove delimited by a pair of ridges on the anterodorsal surface of the premaxilla, a premaxilla with an elongated internarial process that overlies nasal and extends posterior to the external naris, 13 premaxillary teeth with large and incisiviform crowns, the absence of pleurocoels in cervical vertebrae, and an hourglass-shaped metacarpal II, among other features.

Even though the exact aquatic locomotion of Natovenator is unknown, Lee and colleagues suggested that its forelimbs acted as flippers for propulsion when swimming.

[1] The Barun Goyot Formation is regarded as Late Cretaceous in age (Upper Campanian) based on sediments and fossil content.

[5][6][7] The Barun Goyot Formation was also home to many other vertebrates, including the ankylosaurids Saichania, Tarchia and Zaraapelta;[8][9] alvarezsaurids Khulsanurus, Ondogurvel, and Parvicursor;[10][11] birds Gobipipus, Gobipteryx and Hollanda;[12] dromaeosaurids Kuru and Shri;[13][14] fellow halszkaraptorine Hulsanpes;[15] protoceratopsids Bagaceratops and Breviceratops;[16] pachycephalosaurid Tylocephale;[17] oviraptorids Conchoraptor, Heyuannia and Nemegtomaia;[18][19] and the large sauropod Quaesitosaurus.