During the last several decades, wetlands are losing their ecological functions due to increasing anthropogenic loads. One of these functions is the ability to bind elements forming geochemical barriers. The research aimed to study the geochemical conditions of natural wetlands and flooded paddy fields (artificial wetlands) in the Ganjiang River basin to trace geochemical barriers. The research approach was based on a comprehensive analysis of water and aqueous extracts from bottom sediments and paddy soils, including chemical and mineral composition. The samples were collected in November 2019, during the dry season at the end of harvesting. Chemical analysis was performed using standard methods for natural substances: titrimetry, photometry, ionic chromatography, high-temperature oxidation, ICP-MS, and ICP-AES. The mineral composition of the soils and sediments was determined by XRD. It was found that the main physicochemical characteristics (TDS, pH, main component concentrations) of the natural wetland water correspond to the surface water of the study area, whereas the irrigation water is similar to shallow groundwater. The content of trace elements in the irrigation water is higher than in the natural wetland water. Generally, the trace element composition of the natural wetland water corresponds to the geochemical background of the study area. Analysis of the mineral and chemical composition of the paddy soils and sediments indicates the geochemical barriers that accumulate a wide range of elements. In the natural wetland, the geochemical barrier is likely associated with a decrease in oxygen content and advective transport rate in the sediments, whereas in the paddy fields, the precipitation of clay minerals in the soil profile forms the geochemical barrier related to a decrease in filtration properties and advection-diffusion transport.