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Abstract Using nanofluids in photovoltaic‐thermal systems enhances the overall efficiency; however, increasing the pressure drop and pumping power, because of the higher viscosity of nanofluids, is a challenging factor for the nanofluid‐based systems. In the present study, the thermohydraulic performance of the photovoltaic‐thermal system is compared using two water‐based nanofluids including hybrid Ag‐MgO and carbon nanotubes (CNT) nanofluids, as the working fluids. The effect of type and flow rate of the working fluid, nanoparticle concentration, and channel height on the friction factor and Nusselt number is studied using the numerical model. The model is validated using the experimental and numerical results and found that the relative errors of the results are less than 3.8% and 5.2%, respectively, which confirmed the model accuracy. The results showed that at a flow rate of 8 L/h, the volume fraction of 2%, and channel height of 10 mm, the system electrical efficiency, thermal efficiency, and friction factor using CNT nanofluid are, respectively, 0.04%, 1.31%, and 62% higher than those using base fluid and 0.03%, 0.89%, and 53% higher than those using Ag‐MgO nanofluid. It is also found that although increasing the nanoparticle concentration and decreasing the channel height improves the system efficiency, it increases the friction factor and pressure drop. Comparing the results using the mono and hybrid nanofluids showed that the thermal performance of the photovoltaic‐thermal system using CNT nanofluid is slightly better; however, the hydraulic system performance using hybrid Ag‐MgO nanofluid is improved.