Across species, the skeletal system shares mutual functions, including the protection of inner organs, structural basis for locomotion, and acting as an endocrine organ, thus being of pivotal importance for survival. However, insights into skeletal characteristics of marine mammals are limited, especially in the growing skeleton. Harbor seals (Phoca vitulina) are common marine mammals in the North and Baltic Seas and are suitable indicators of the condition of their ecosystem. Here, we analyzed whole-body areal bone mineral density (aBMD) by dual-energy X-ray absorptiometry (DXA) and lumbar vertebrae by high-resolution peripheral quantitative computed tomography (HR-pQCT) in neonate, juvenile, and adult harbor seals. Along skeletal growth, an increase in two-dimensional aBMD by DXA was paralleled by three-dimensional volumetric BMD by HR-pQCT, which could be attributed to an increasing trabecular thickness while trabecular number remained constant. Strong associations were observed between body dimensions (weight and length) and aBMD and trabecular microarchitecture (R2 = 0.71-0.92, all p < 0.001). To validate the results of the DXA measurement (i.e., the standard method used worldwide to diagnose osteoporosis in humans), we performed linear regression analyses with the three-dimensional measurements from the HR-pQCT method, which revealed strong associations between the two imaging techniques (e.g., aBMD and Tb.Th: R2 = 0.96, p < 0.0001). Taken together, our findings highlight the importance of systematic skeletal investigations in marine mammals during growth, illustrating the high accuracy of DXA in this context. Regardless of the limited sample size, the observed trabecular thickening is likely to represent a distinct pattern of vertebral bone maturation. As differences in nutritional status, among other factors, are likely to affect skeletal health, it appears essential to routinely perform skeletal assessments in marine mammals. Placing the results in the context of environmental exposures may allow effective measures to protect their populations.