Enhydra fluctuans Lour. is consumed by various tribes in their ethnomedicinal practices for the treatment of kidney stones and urinary problems. However, no scientific studies were conducted to evaluate its effect on crystal growth. Hence, the present study proposed to investigate the effect of aqueous extract of whole plant of standardized E. fluctuans (AEEF) on the growth of calcium phosphate (brushite) crystals. Attempts were also made to evaluate the effect of in vitro free radical scavenging and antimicrobial activities of AEEF. In vitro studies indicated that AEEF (50, 100, and 200 µg/mL) exhibited an inhibitory role on brushite crystal growth. The average length of the deposited brushite crystals was decreased by citric acid (1molL−1) and AEEF (200, 100, and 50 µg/mL) till day 8. Results showed that AEEF (200 and 100 µg/mL) and citric acid significantly (P<0.001) decreased the crystal bed as compared to the control on day 8 of the study. AEEF showed an antimicrobial effect against Staphylococcus aureus and exhibited antioxidant activity. In conclusion, the aqueous extract of the whole plant of Enhydra fluctuans was found effective in the inhibition of brushite crystals. Further, in vivo studies along with molecular studies and bioactivity-guided fractionation are required to strengthen its antilithiatic effect along with identifying the bioactive compounds and the mechanism of action involved therein.