The biological diversity of zooplankton communities was studied in August 2006 and 2007 in Lake Łuknajno (Masurian Lakeland, NE Poland), a shallow, macrophyte-dominated water body. An analysis of the species composition, abundance, biomass and the values of biocoenotic indices revealed significant differences between the analyzed zooplankton groups. The noted differences were related to trophic levels, the presence of macrophytes and environmental conditions. A total of 20 zooplankton species were reported in 2006 and 2007. The average abundance and biomass of zooplankton in 2006 and 2007 reached 546 indiv./dm3 and 0.3085 mg/dm3, and 385 indiv./dm3 and 0.6113 mg/dm3, respectively. Rotifers dominated in terms of abundance (75% in 2006 and 70% in 2007), while crustaceans in terms of biomass (approx. 80% in 2006 and over 70% in 2007). In 2006 and 2007, indicator species of high trophicity accounted for 41% and 24%, respectively, of the total zooplankton abundance in Lake Łuknajno. The values of biocoenotic indices did not point to the predominance of any zooplankton group. There were no significant differences in biodiversity between sites with and without macrophyte cover, whereas such differences (p < 0.05) were observed between sampling sites.