The mathematical modeling of simultaneous shrinkage and shape change (deformation) during drying of gel model systems (GMS) was investigated. Developed theory was applied to estimate water diffusivities during drying of GMS (70 °C, air velocity of 2 m/s) shaped as square prisms (9.53 mm × 9.53 mm × 80 mm) and longitudinal sections (quarters and halves) of cylinders (12.7 mm diameter × 140 mm length) by considering the product shrinkage with and without deformation. The contours of transversal product slices, obtained from digital images, were averaged to extract relevant characteristics of the dried samples, whereas compactness and roundness were used to evaluate product deformation. Experimental shape patterns were used to estimate the initial and final mesh matching the real product geometry during simulation via a new algorithm. The obtained results demonstrate that although shrinkage occurs from the beginning of drying, changes in product shape are noticeable only after the free moisture fraction is below 0.3. Water diffusivities estimated considering the shape change of product were in the narrow range of 3.37–3.58 × 10−10 m2/s for studied geometries, and are overestimated in about 6–12% when this phenomenon is not included in drying model. No significant differences were observed in water diffusivity values between studied geometries (p > 0.05). •Drying of cylinder sections and square prisms made from gel was studied.•Image analysis was used to characterize shrinkage and deformation of samples.•A new algorithm was used to create a mesh matching the real product shape.•Shape change and moisture profiles during drying were simulated.•The effect of geometry and deformation on water diffusivity was appraised.