Water treatment systems in swimming ponds support the natural self-cleaning capabilities of water based on the functions of repository macrophytes in their regeneration zone and the regulation of the internal metabolism of the reservoirs. As part of the project, a functional modular filtration chamber with system multiplication capabilities was designed and created. This element is dedicated to water treatment systems in natural swimming ponds. The prototype system consisted of modular filtration chambers and pump sections, as well as equipment adapted to the conditions prevailing in the eco-pool. An innovative solution for selective shutdown of the filtration chamber without closing the circulation circuit was also used, which forms the basis of a patent application. A verified high-performance adsorbent, Rockfos® modified limestone, was used in the filtration chamber. In order to determine the effective filtration rate for three small test ponds with different flow rates (5 m/h, 10 m/h and 15 m/h), the selected physicochemical parameters of water (temperature, pH, electrolytical conductivity, oxygen saturation, total hardness, nitrites, nitrates, and total phosphorus, including adsorption efficiency and bed absorption capacity) were researched before and after filtration. Tests were also carried out on the composition of fecal bacteria and phyto- and zooplankton. Based on high effective phosphorus filtration efficiency of 32.65% during the operation of the bed, the following were determined: no exceedances of the standards for the tested parameters in relation to the German standards for eco-pools (FLL—Forschungsgesellschaft Landschaftsentwicklung Landschaftsbau e. V., 2011); lower number of fecal pathogens (on average 393—coliform bacteria; 74—Escherichia coli; 34—fecal enterococci, most probably number/100 mL); the lowest share of problematic cyanobacteria in phytoplankton (<250,000 individuals/dm3 in number and <0.05 µg/dm3—biomass); low chlorophyll a content (2.2 µg/dm3—oligotrophy) and the presence of more favorable smaller forms of zooplankton, an effective filtration speed of 5 m/h. This velocity was recommended in the FLL standards for swimming ponds, which were adopted in this study as a reference for rapid filters. In testing the functional efficiency of a dedicated filtration system for a Type II test pond (50 m2—area and 33 m3—capacity), at a filtration rate of 5 m/h, an average effective phosphorus adsorption efficiency of 18.28–53.98% was observed under the bed work-in-progress conditions. Analyses of other physicochemical water parameters, with appropriate calculations and statistical tests, indicated progressive functional efficiency of the system under bathing conditions.