The Musi River, the largest river in Palembang in South Sumatera, has become one of its important sites, in which various activities such as shipping and irrigation are performed. Those activities are assumed to eventually affect the fertility of the waters. This research was conducted to accomplish three targets. The first was to analyze the abundance, diversity index (H'), uniformity (E), and the dominance of phytoplankton and zooplankton. The second target was to examine the difference in abundance of phytoplankton and zooplankton in the stations using ANOVA. The third was to analyze the relationship between the abundance of phytoplankton and zooplankton using PCA (Principal Component Analysis). Results revealed that the phytoplankton found downstream of the Musi River consisted of four classes. Bacillariophyceae, for instance, dominated the waters with a rate of 51.35%, followed by Chlorophyceae with a rate of 33.58% and the other two classes. The zooplankton consisted of twelve classes whose dominant class was Cilliate reaching 36.56% and followed by Mastigophora of 14.7%. It was also discovered that the diversity index (H') of plankton was moderate. Results indicate that the water condition was somewhere in between moderately and heavily polluted. The uniformity index (E) was high while the level of dominance (D) indicates that there was no dominant genus in the waters. Moreover, based on ANOVA, the abundance of plankton in the stations showed no significant differences. In addition, the abundance of zooplankton was influenced by four factors whose largest contribution was nitrite, TSS, and fosfat reaching 37.2%.