This study developed an eco-friendly and integrated strategy to treat malachite green (MG) pollution using green-synthesized ZnO–TiO2 nanocomposites (NCs), followed by phytoremediation with Lemina minor. The ZnO–TiO2 NCs were synthesised via a one-pot green chemistry approach using Aporosa cardiosperma leaf extract, and thoroughly characterised through UV–vis spectroscopy, FT-IR, DLS-Zeta potential analysis, FE-SEM, HR-TEM, XPS, and TGA/DSC. These NCs demonstrated high photocatalytic efficiency, achieving 91.05% degradation of MG under sunlight and 74.79% under UV light within 60 minutes, along with strong reusability across treatment cycles. Then, in dye-treated water, degraded dye residues and NCs were present. They were absorbed by L. minor, aiding in water purification. Toxicity evaluation using Daphnia magna revealed significant morphological and cellular damage upon MG exposure, while ZnO–TiO2 NCs provided moderate mitigation. Remarkably, subsequent treatment with L. minor dye-treated water preserved organism health, as confirmed through CLSM and SEM-EDS analyses, indicating effective pollutant removal and reduced toxicity. Water quality parameters, including pH, dissolved oxygen, BOD, total solids, and hardness, showed notable improvements after treatment, aligning with global standards for safe drinking, agriculture, and aquaculture use. This study highlights a sustainable, nature-based approach for effective pollutant removal and water quality restoration, supporting broader environmental conservation and circular water management applications.