This study evaluated the cytotoxic effects of methanol and water extracts from Bacopa monnieri (L.) Wettst and Ceratophyllum demersum L. on HepG2 (liver cancer) and THLE2 (normal liver) cell lines using XTT assay. The extracts were tested at concentration range of 12.5-400 µg/mL. In HepG2 cells, the water extract of B. monnieri at 400 µg/mL exhibited the highest cytotoxicity, reducing cell viability to 11.08%, which was statistically significant (p < 0.05) compared to other treatments. The methanol extract of C. demersum at 12.5 µg/mL had the least effect, maintaining 94.84% cell viability. For THLE2 cells, the water extract of B. monnieri (400 µg/mL) also showed the greatest reduction in cell viability (30.85%). The water extract of C. demersum at the same concentration resulted in similar viability (32.01%), with no significant statistical difference (p > 0.05). The lowest concentrations of methanol and water extracts of C. demersum showed minimal effects (97.55% and 97.74% viability, respectively). Median inhibitor concentration (IC50) analysis revealed that B. monnieri’s water extract was most effective, with IC50 values of 68.45 µg/mL for HepG2 and 127.05 µg/mL for THLE2 cells. In contrast, C. demersum’s methanol extract had the highest IC50 values (173.35 µg/mL and 228.46 µg/mL, respectively), indicating lower cytotoxicity. Heatmap and cluster analyses highlighted the selective cytotoxicity of C. demersum on cancer cells with minimal effects on normal cells, showing its potential for targeted cancer therapy.