A total of 44 bacterial species were isolated; 28 were Gram-positive and 16 were Gram-negative bacteria. Terengganu River recorded the highest number of bacterial isolation with 506 isolates, followed by Pedu Lake with 286 isolates and Kenyir Lake with 179 isolates. Isolates from Terengganu River were from 41 different species of bacteria compared to 25 different bacteria species recorded in Kenyir and Pedu lakes, respectively. The three highest bacteria species isolated were Streptococcus agalactiae(275 isolates; 28.3%), Lactococcus lactis (82 isolates; 8.4%) and Micrococcus spp. (71 isolates; 7.3%). The bacteria species with lowest presence (2 isolates; 0.2%) were Enterococcus faecalis, Gemella haemolysans, Pasteurella spp., Proteus mirabilis, Salmonella spp. and S. constellatus. The details on the isolated bacteria, their number and percentages in each sampling sites are presented in Table 1.