This study indicates that in the wastewater treatment plant “Wschód” in Gdańsk, working in the modified UCT system, the effectiveness of bacteria pollutant removal varies from 92 to 99% and almost 100% of parasites are removed. Despite this, the number of indicator bacteria and periodical presence of Salmonella in the effluent indicates that it is strongly bacteriologically polluted. It was discovered that the number of indicator bacteria in primary sludge was by 1 to 3 orders of magnitude higher than in the excess activated sludge. Also, Salmonella was twice more frequently detected in the primary sludge than in excess activated sludge (70% and 30%, respectively). In contrast, the average number of invading helminths’ ova (ATT) was over two times higher in excess activated sludge than in primary sludge. An efficient method for controlling activated sludge bulking resulting from intensive growth of Microthrix parvicella was dosing of PAX-16 (the doses from 2.5 to 4.8 g Al3+/kg d.m.·d).