In recent years, research trends are concentrated towards nanoparticles in many fields like aquatic ecosystems, clinical and pharma, agro and food chain-based industries. Nanomaterial plays a very crucial role in all the above fields, very particularly in medical treatments and experiments, aquatic ecosystems. The current study is to examine the ecological effects of nanoparticles in a commensal-host aquatic model with commensal species interference with the effect of nanoparticles. We examined the direct and indirect influence of these particles on the proposed model in view of stability of the system with appropriate chosen attributes. Our findings are more focused on nanoparticle-induced aquatic ecosystem which may stabilize or destabilize the system, resulting in sensitive analysis through various parametric values. We also found that as the contact rate between nanoparticles and the host increases, the equilibrium densities of the host and commensal fall. Furthermore, we notice that the depletion of nanoparticles from the aquatic system plays a vital role for the steady coexistence of both populations. Finally, the analytical results are verified and exposed through computer simulations which are quite interesting.