Uncertainties in mathematical modelling of water transport in cereal grain kernels during drying and storage are mainly due to implementing unreliable values of the water diffusion coefficient and simplifying the geometry of kernels. In the present study an attempt was made to reduce the uncertainties by developing a method for computer-aided identification of the water diffusion coefficient and more accurate 3D geometry modelling for individual kernels using original inverse finite element algorithms. The approach was exemplified by identifying the water diffusion coefficient for maize kernels subjected to drying. On the basis of the developed method, values of the water diffusion coefficient were estimated, 3D geometry of a maize kernel was represented by isoparametric finite elements, and the moisture content inside maize kernels dried in a thin layer was predicted. Validation of the results against experimental data showed significantly lower error values than in the case of results obtained for the water diffusion coefficient values available in the literature.