Aquatic birds represent diverse ecologies and locomotion types. Some became flightless or lost the ability for effective terrestrial locomotion, yet, certain species excel in water, on land, and in air, despite differing physical characteristics associated with each medium. In this exploratory study, we intend to quantitatively analyze the morphological variety of multiple limb bones of aquatic birds using 3D geometric morphometrics. Morphological variation is mainly driven by phylogeny, which also affects size and locomotion. However, the shape of the ulna, including the proportion and orientation of the epiphyses is influenced by size and aquatic propulsive techniques even when phylogeny is taken into consideration. Certain trends, possibly linked to functions, can be observed too in other bones, notably in cases where phylogenetic and functional signals are probably mixed when some taxa only englobe species with similar functional requirements: penguins exhibit the most distinctive wing bone morphologies, highly adapted to wing‐propulsion; advanced foot‐propellers exhibit femur morphology that reduces proximal mobility but supports stability; knee structures, like cnemial crests of varied sizes and orientations, are crucial for muscle attachments and efficient movement in water and on land; taxa relying on their feet in water but retaining terrestrial abilities share features enabling swimming and walking postures. Size‐linked changes distinguish the wing bones of non‐wing‐propelled taxa. For hindlimbs, larger size relates to robust bones probably linked to terrestrial abilities, but robustness in femora can be connected to foot‐propulsion. These results help us better understand birds' skeletal adaptation and can be useful inferring extinct species' ecology.