Landfilling of municipal solid waste generates a number of problems. This article focuses on one of them – the settling of the landfill surface due to organic residue biodegradation. The task of predicting the settlement of the waste storage surface is proposed to be solved within the framework of the theory of filtration consolidation of porous media. Accordingly, the problem of the dynamics of methane and carbon dioxide emission into the atmosphere was solved on the basis of known experimental data. The application of the proposed approaches made it possible to avoid modeling microbial dynamics and determining the stress-strain state of the waste storage massif, which would significantly complicate the mathematical model of the problem. Numerical solutions of the corresponding boundary value problem in a variable-time domain were found using the finite element method. Numerical experiments show changes in the dynamics of waste storage surface settlements for the case of taking into account biodegradation effects.