Microchannel heat sinks (MCHSs) have drawn much interest from the scientific community for thermal management. They are known as an effective cooling technique among several newly developed methods for dissipating high heat. This study investigates the thermal and hydrodynamic characteristics of square and circular micro-pin fin arrays to maximize heat dissipation in open-type MCHSs with water-based coolants, including different nanoparticle shapes. The nanoparticle shapes studied are spherical, plate, blade, and cylindrical. The most effective nanoparticle and pin-fin shape are identified according to the heat transfer enhancement and pressure drop. The numerical results show the significant effect of pin-fins on the temperature distribution over the target channel. The MCHS with circular pinfins has the lowest temperature. For nanofluids, while the channel with square pin-fins has a thermal performance factor of 1.45, circular pin-fins provide a maximum thermal performance factor of 1.57. As the velocity and particle volume concentration of nanofluids increase, the convective cooling becomes more pronounced. The maximum thermal performance factor of 1.05 is found in the spherical alumina-water nanofluid at 4% concentration. Numerical results show that the maximum heat transfer is obtained in the case of platelet nanoparticles, while it noticeably increases pressure drop. The nanofluid containing blade-shaped nanoparticles has the highest thermal performance factor of 1.33 at a volume percentage of 4%.