Mathematical modeling and computer simulation methods have been used to investigate the extent of influence exerted by bio-clogging on the dynamics of excess head scattering in the soil massif. To this end, the classical equation of filtration consolidation has been modified for the case of variable porosity resulting from changes in the biomass. The numerical solution to the constructed mathematical model in the form of a nonlinear boundary problem was derived by a finite-element method. Numerical experiments were carried out and their analysis was performed. Specifically, this paper shows the charts of pressure differences in the soil array when neglecting bio-clogging and when estimating the effects exerted by bio-clogging at specific points in time. The numerical experiments demonstrated that in two years after the onset of the consolidation process in the neighborhood of the lower limit of the examined soil mass with a thickness of 10 meters, excess heads fall from the initial value of 10 m to 4 m. The greatest impact from the clogging of pores by microorganisms is revealed in the neighborhood of an upper limit. At a depth of 1 m, at t=180 days, the pressure difference reaches 2.4 m. This is about 200 % of the pressure distribution without taking into account the effects of bio-clogging. Over time, the effect of bacteria on the distribution of pressures in the neighborhood of the upper boundary decreases. However, this effect extends to the entire soil mass, up to the lower limit. Thus, at t=540 days, at the lower limit, the effect of bio-clogging leads to that excess heads are 1.8 m greater than for the case of pure water filtration (a relative increase of about 80 %). Bio-clogging processes are intensified as a result of the development of microorganisms when organic chemicals enter the porous environment. Therefore, from a practical point of view, studying them is especially relevant for household waste storage facilities and the stability of their soil bases. It is advisable to undertake research by using the methods of mathematical modeling and computer simulation