The influence of different functional covalent groups on the thermophysical properties of carbon nanotube-base fluid was first investigated experimentally. To shed more light on this issue, cysteine (Cys) and silver (Ag) were covalently attached to the surface of the multi-walled carbon nanotubes (MWCNT). Functionality and morphology were studied by the aid of characterization instruments to confirm surface functionalization, as well. To calculate the thermal properties, different water-based nanofluids such as Gum Arabic-treated multi-walled carbon nanotubes (MWCNT-GA), functionalized MWCNT with cysteine (FMWCNT-Cys) and silver (FMWCNT-Ag) were employed as coolants to investigate the convection heat transfer coefficient, Nusselt number, friction loss, pressure drop and pumping power in a counter flow corrugated plate heat exchanger. Calculations were performed for Reynolds numbers ranging from 2500 to 10,000 (turbulent flow) and nanoparticle weight percentages of 0.0% to 1.0% using a FORTRAN code. Nanofluid properties were also measured through experimentation. It was found that increasing Reynolds number, Peclet number or fraction of nanomaterial would improve the heat transfer characteristics of the nanofluid. However, for a specific material, augmentation of Reynolds number or nanomaterial fraction would cause the required pumping power to rise but this penalty was relatively small. In all the investigated cases, heat transfer rate and power consumption were found to be less for water compared to nanofluids. Besides, heat removal in nanofluids was discovered to be higher than that of water for a specific pumping power. Therefore, performance of the plate heat exchanger can be enhanced by choosing MWCNT/water as the working fluid.