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The study on the structure of the plankton community in monoculture and Integrated Multi-Trophic Aquaculture System (IMTA) Floating Net Cages at Karimunjawa Islands was conducted in October 2021. This study aimed to assess the structure of the plankton community along with water quality parameters in those areas. Sampling was carried out by using the filtration method with a plankton net at three locations, namely monoculture, IMTA floating net cages, and non aquaculture (reference site). The study discovered 40 species consisting of 22 species of phytoplankton and 18 species of zooplankton. The phytoplankton found were from the Bacillariophyceae, Cyanophyceae, and Dinophyceae classes, while the zooplankton were from the Ascidiacea, Branchiopoda, Eurotatoria, Hexanauplia, Malacostraca, Secementea and Thecostraca classes. The biological indeces of phytoplankton showed the diversity index (H) between 1.26 - 2.27, the evenness index (E) between 0.4-0.17, and the dominance index (D) between 0.46 - 0.72. The zooplankton biological indeces showed the value (H) between 1.44-2.28, the value (E) is between 0.67 - 0.99 and the value (D) is between 0.11-0.19. Water quality parameter ranges were: visibility 5.1-7.38 m, water temperature 24.53-25.8 °C, turbidity 0-0.48 NTU, DO 1-14.74 mg.L−1, pH 5.75-9.55, salinity 29.5-33 °/oo and TDS 8.94 - 18.9 ppm. The results of the parametric data test using one way analysis of variance (ANOVA) showed that the abundance of plankton structure at the three locations was significantly different (p