The subject of the study were the benthic diatom communities of the Puck Bay littoral zone. Samples of the sediments were taken from sites situated near the sewage treatment plant at Swarzewo from June 1998 to May 1999. The analysis of the species composition and the relative percentages of the diatom indicative groups were used to evaluate water quality. The following ecological factors were taken into consideration: salinity, trophic status and saprobity. Following Lange?Bertalot (1979), water quality was classified based on a 5-degree scale of saprobity. It was correlated to the percentages of the sensitive, tolerant and resistant diatoms taxa and their reaction to organic matter content. The water quality evaluation was tested with the diatom indices using Omnidia 3 software. The results of the diatom studies indicate that the dominating groups were the oligohalobous and mesohalobous taxa, which are characteristic of eutrophic waters and contain biogenic compounds, mainly nitrogen and phosphorus. The most abundant groups in the saprobic spectrum were the resistant (-mesosaprobic, polysaprobic) and tolerant (-mesosaprobic, /-mesosaprobic) diatoms, which are indicators of water purity class II (III), and in summer, predominantly class III. The comparison of the results of diatom analysis of the Puck Bay microphytobenthos obtained with the Lange?Bertalot (1979) method and the those acquired with Omnidia 3 software demonstrates the possibility of applying it to evaluate environmental status and assess polluted brackish waters.