<p>Swimming is a popular sport with several health benefits, but its effects on bone quality are controversial possibly due to distinct effects on different anatomical regions. Our aim was to investigate the effect of 8-month swimming on bone growth, mass, geometry, trabecular microarchitecture and osteocyte density of the lumbar vertebrae, femur and tibia of male rats. Wistar rat models were assigned to either a swimming (<i>n</i> = 10; 2h/d, 5 d/week) or a physically active control group (<i>n</i> = 10) for 8 months, after which they were sacrificed and their lumbar vertebrae, femur and tibia assessed for bone mass, cortical geometry, trabecular microarchitecture and osteocyte density through <i>µ</i>-CT and histology. Variables were compared between groups through independent samples <i>t</i> tests. Swimming animals displayed higher vertebral trabecular connectivity and lower trabecular separation compared to controls. However, femur length, trabecular and cortical bone mass and cortical thickness were lower compared to controls. At the tibia, animals from the swimming group also presented lower trabecular number and connectivity and higher trabecular separation. Osteocyte density at the femur and vertebra was similar between groups. Eight months of swimming negatively affected bone mass, cortical geometry and trabecular microarchitecture at the femur and tibia whilst having a favourable effect on vertebral trabecular microarchitecture. These results suggest that swimming has divergent effects on different anatomical regions.</p>