In the paper, computational homogenization approach is used for recognizing the macroscopic permeability from the microscopic representative volume element (RVE). Flow of water, at both macro and micro level, is assumed to be ruled by Darcy law. A special averaging constraint is used for numerical flow analysis in RVE, which allows to apply macroscopic pressure gradient without the necessity to use directly Dirichlet or Neumann boundary conditions. This approach allows arbitrarily shaped representative volumes and eliminates undesirable boundary effects. Generated effective permeability takes into account the structuring effects, what is an advantage over other homogenization methods, like self-consistent one.