Abstract A numerical investigation is performed to study the effects of different nanofluids on the thermal and flow fields through transversely wavy wall channels with different phase shifts between the upper and lower wavy walls. Reynolds numbers are considered in the turbulent range of 6000 ≤ Re ≤ 18,000 and a uniform wall temperature of 400 K is applied on the walls. The two dimensional continuity, Navier–Stokes and energy equations are solved by using finite volume method (FVM). The optimization was carried out by using various phase shifts (θ = 0°, 30°, 60°, 90° and 180°) and three different wavy amplitudes (α = 0.5, 1 and 1.5 mm) to reach the optimal geometry with the maximum performance evaluation criterion (PEC). The main aim of this study is to analyze the effects of SiO2 nanoparticles, its concentration (1–4%), and nanoparticle shapes (i.e. blades, platelets, cylindrical, bricks, and spherical), on the heat transfer and fluid flow characteristics. Simulation results show that the wavy channel performance was greatly influenced by changing the phase shift and the wavy amplitude. The highest PEC was obtained for the phase shift of θ = 30° with α = 0.5 at Re = 6000. It is found that the SiO2-EG nanofluid with platelets nanoparticle shape gives the highest heat transfer enhancement compared with other tested nanofluids.