Abstract. The restoration technologies of biological soil crust (BSC) in arid and semi-arid areas can be supported by simulations performed by mathematical models. The present study represents a mathematical model to describe behaviour of the complex microalgae development on the soil surface. A diffusion-reaction system was used in the model formulation which incorporating parameters of photosynthetic organisms, soil water content and physical parameter of soil porosity, extendable 10 for substrates and exchanged gases. For the photosynthetic microalgae, the dynamic system works as a batch mode, while input and output are accounted for soil water-limited substrate. The coupled partial differential equations (PDEs) of model were solved by numerical finite-element method (FEM) after determining model parameters, initial and boundary conditions. The MATLAB features, were used in solving and simulation of model equations. The model outputs reveals that soil water balance shift in microalgae inoculated lands compare to bare lands. Refining and application of the model for the biological 15 soil stabilization and the biocrust restoration process will provide us with an optimized mean for biocrust restoration activities and success in the challenge with land degradation, regenerating a favourable ecosystem state, and reducing dust emissionrelated problems in the arid and semi-arid areas of the world.