Research carried out from 2007 to 2011 showed that a tested semi-natural water system with a diverse catchment (peat, peat-mineral and mineral) has a very varied quality of water, as evidenced by a the large range of conductivity (174-828 μS/cm) and pH (6.34-9.92). Natural lake parts of the semi-natural water system were similar to the artificial parts in terms of physico-chemical parameters, as evidenced by the lack of statistically significant differences between the water quality in both of these ecosystems. Taking into account the quality of various types of water in this semi-natural system, it can be seen that the river waters differed significantly (p < 0.001) in concentrations of biogenic elements (nitrogen, phosphorus) from another type of ecosystems. In addition, rivers poor in organic matter (TOC < 10.0 mg/L) which directly supplied the water system contributed to higher values of many tested parameters (EC, pH, TC, TN, SO4 (2-) or Cl(-)) in waters of the canal. In contrast, rivers with high values of concentrations of organic matter (TOC > 10.0 mg/L) contributed to a decline in values of those parameters. Moreover, lake waters within the tested semi-natural water system showed a "cleansing" function, because they caused a decrease in conductivity, pH or the concentration of carbon, total nitrogen, sulphate(VI) and chloride in waters of the canal.