This study was carried out to analyze the group of secondary metabolites of leaf extract of Nypa fruticans which can be bioactive compounds to pathogenic bacteria Aeromonas hydrophila, Pseudomonas aeruginosa, and Escherichia coli. It was carried out from March to April 2021, and samples were collected from Mengkapan Village, Sungai Apit District, Siak Regency, Riau Province, Indonesia. The method used in this study was experimental, using a completely randomized design (CRD) with 1 factor (leaf extract concentration) with 4 treatment levels, namely 12.5%, 25%, 50%, and 100%, paired with negative and positive control with 3 replications. The bioactive substances were extracted by using ethanol solvent. The effectiveness of antibacterial substances was measured using the paper disc diffusion agar method. The phytochemical analysis released that leaf extract contained alkaloids, phenolics, flavonoids, tannins, terpenoids. The extract inhibited the growth of pathogenic bacteria A. hydrophila, and P. aeruginosa very strongly (inhibition zone >20 mm), with inhibition diameters ranging from18.56-26.16 mm and 21.00-28.10 mm, respectively. Meanwhile, for E. coli, the inhibitory zone was weak (< 5 mm), in which the diameter of inhibition ranged from 2.80-6.46 mm.