The noise issue, especially in industrial scale systems including nuclear power plants, there has been always an interesting subject in system stability analysis. In this paper the effects of fluctuations in coolant temperature and velocity at the inlet of a fuel assembly of a VVER-1000 reactor with Al2O3 nanofluid coolant water were investigated. This analysis is performed by using a Fourier transformed conservation equation (mass, momentum and energy) in frequency space. The transformed equations were discretized with finite volume method and numerically solved. Thermodynamic properties of nanofluid were evaluated by adding new subroutines to IPAWS IF97 steam table libraries. The comparison between the achieved results of the applied model and previous studies performed with porous media approach and COBRA-EN code, showed a good agreement. Thermal-hydraulic effects of nanofluid on noise fluctuations were calculated based on different concentrations of Al2O3 nanoparticle and noise frequencies. Calculations showed that any increment in nanoparticles mass fraction will result in reduction of fluctuations in coolant temperature and velocity.