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Drying is typically evaluated considering a pure diffusional process in an isotropic sample. However, biological materials are anisotropic, and their structural elements can affect the water flow during processing. In this work, the effect of microstructure elements on sample deformation, drying and rehydration processes (kinetics and mechanisms) was evaluated, using pumpkin cylinders (formed mainly of parenchyma and xylem tissues). The cylinders were obtained considering a transversal (Tc) and longitudinal (Lc) cut orientation. The orientation of the xylem vessels did not affect the drying kinetics (both orientations showed similar k and n parameters of Page model). However, it had a significant impact on deformation. The Lc-samples showed more uniform appearance than the Tc ones. Tc showed a tendency towards black in the grey intensity histogram and higher density in the X-ray analysis. The Lc-samples presented the highest rehydration rate (k1 of Peleg model: 2.87 ± 0.16 min d b−1). In contrast, higher equilibrium moisture was observed in samples with Tc (k2 of Peleg model: 0.078 ± 0.003 d b−1). The results showed the anisotropicity of biological materials, and how the microstructural elements affect the mass transfer. Additionally, a water transport mechanism by capillarity through the xylem vessels during drying and hydration was demonstrated.