The aim of this study was to analyse the impact of velocity in the hydroponic lagoon used as the 3rd stage of municipal wastewater treatment on washing out of the particles suspended in the sewage as well as settled on the bottom of the hydroponic ditch. In order to analyse the flow velocity in the lagoon, 12 cross-sections were determined at points where the speed and motion of particles can change. Wastewater samples were taken in the summer month from each of the 12 sampling points (the depth of 0.1 m) and the basic physicochemical parameters of sewage were determined (BOD5, COD, TOC, TSS, turbidity). In selected cross-sections, a granulometric analysis of particles was made to determine the characteristics of suspended solids in the wastewater flow path. Based on the analysis, it was found that velocities in the lagoon during aeration can be ten times higher (0.070 m·s−1) than those assumed by designers (0.006 m·s−1). Such a large difference means that the sedimentation conditions assumed in the project cannot be met, which may result in an increase in the total suspended solids and organic matter concentrations at the outflow to the receiving water body. During the flow through the hydroponic ditch, the highest efficiency of pollutant removal was indicated for BOD5 — 88.7% and TSS — 80%, while the COD removal occurred with the lowest efficiency — 34.1%. Improving flow conditions as designed in the hydroponic lagoon technological project may increase the efficiency of wastewater treatment at the third stage of treatment.