Construction in waterlogged areas requires special design solutions and expensive site preparation works. Operating experience shows that the efficiency of drainage systems in peat soil decreases over time. This article describes factors to be taken into account when designing drainage systems in peat soil. It also summarizes the results of the laboratory surveys for peat and filling material permeability reduction over time. We used a laboratory box to study water permeability over time. In the experiment, we used poorly decomposed peat of natural structure and compacted peat. The study found that the water inflow into the drainage system decreased 1.5 to 1.7 times in the course of filtration. The greatest peat permeability reduction was recorded at the initial stage. The article demonstrates how the grain-size composition of sand used as backfilling affects its water permeability. In order to ensure normal operation of drainage systems in peat soil, one must consider the reduction of peat water permeability over time and clogging of sand filling when designing the said systems.