The purpose of this research was to examine water treatment improvement by using natural powdered zeolite (clinoptilolite). Experiments were carried out at a laboratory and in a pilot-scaled water treatment plant. The pilot-scaled plant was fed with groundwater containing a high level of organic compounds from the existing waterworks in Lithuania’s Neringa Region. The content of organic substances in the groundwater – characterized by chemical oxygen demand (COD), varied between 5.0 – 40.0 mg O₂ 1^-1 and the permanganate index (oxidation by potassium permanganate) 4.0 – 8.0 mg O₂ 1^-1 was determined during this case study. There was no significant reduction using conventional water treatment. Laboratory analysis of water quality showed: total iron, ammonium, aluminium residual concentrations, pH, colour (Pt scale), turbidity, COD and permanganate index. The drinking water had an undesirable colour, taste and odour due to high concentrations of organic substances in the groundwater. A fluidized batch process and adsorption of natural powdered zeolite were used for reducing organic substances in the water with the effectiveness of total iron concentration reduction by 96%. Experimental research results are included in the article.