This study aimed to investigate the allelopathic effect of live Egeria densa Planch. and its aqueous extracts in inhibiting the cyanobacterium Microcystis aeruginosa (Kützing) Lemmermann through a possible growth inhibition pathway. Under coexistence, the presence of live E. densa reduced the growth of M. aeruginosa by 48% compared to when M. aeruginosa was alone. Consequently, we prepared two separate aqueous extracts with distilled water: one from E. densa plants collected from monocultures, and the other from E. densa plants collected from co-cultivation with M. aeruginosa. At a concentration of 0.5 g/L, both extracts successfully suppressed the growth of M. aeruginosa throughout the 5-day exposure period. The extracts obtained from E. densa plants grown in a combined culture with M. aeruginosa showed significant growth-inhibiting capabilities compared to the extracts obtained from E. densa monoculture (p < 0.05). They showed 22% more growth inhibition compared to cultures exposed to monoculture extracts at day 5, indicating that the production of allelochemicals in E. densa was induced during co-existence with cyanobacteria. However, the higher concentrations (2 and 4 g/L) of both extracts did not effectively exhibit a successful inhibitive ability, possibly due to the presence of high nutrient concentrations, specifically PO43−, which may be potentially suppressing the activity of allelochemicals. Further studies are recommended in identifying the specific allelochemicals and exploring their practical implementation in the field.