Chemically functionalized multi-walled carbon nanotubes (F-MWNTs) offer a lot of potential as a novel effective filter due to their unique qualities such as chemical stability, thermal permanence, and high surface area. This study aims to investigate the efficiency of F-MWNTs filters to improve the aquatic conditions for the freshwater bivalve, Mutela singularis (M. singularis). It was shown that the removal performance of F-MWNTs filters for the heavy metals Co, Cu, Fe, Pb, and Zn is favorable at high pH, while Cd, Ni, and Cr are removed at low pH from aqueous solutions. F-MWNTs-based filters removed 99.8% of copper with a 5 μg/L concentration at pH=10. The mechanisms underlying F-MWNT filtration as a feature of pH were discussed. The histological and biochemical composition of M. singularis was studied before and after the use of F-MWNT filters. M. singularis samples in purified conditions had a high standard of structure, as well as a large increase in carbohydrate, lipid, and protein content, for example, the protein increased by 45%. The advancement of wastewater treatment with F-MWNT filters has high expectations. Our research contributes significantly to water treatment applications, and to the potential feeding fields.