Induced water hyacinth with purple roots (PRWH) exerts a significant inhibitory effect on the growth of blue-green algae. Interestingly, its chemical constituents differ from those of wild-type water hyacinth and have not yet been reported. This study aimed to explore the chemical constituents of PRWH and its bioactive components serving as allelopathic agents against blue-green algae. Phytochemical investigation of the bioactive ethyl acetate fraction of a crude methanol extract from PRWH led to the isolation of 56 compounds, including 11 new phenylphenalene derivatives. The structures of these compounds were elucidated by comprehensive analyses through NMR, HRMS, and X-ray techniques. Bioactivity evaluation against Microcystis aeruginosa indicated that compounds 7, 12, 15, 37, 39, 45, and 47 potently inhibited blue-green algae growth.