ZnO nanostructures are well-known photocatalysts for the degradation of toxic organic dyes and their morphology, size, and other physicochemical properties play important roles in their photocatalytic performance. To study the effect of size, morphology, and synthesis conditions in photocatalytic performance, we synthesized ZnO nanoparticles of different morphologies through a simple microwave-assisted chemical process at different pH values of the reaction mixture. Different pH values of the reaction mixture produced ZnO nanoparticles of different morphologies and sizes. The nature of the pH controlling agent and final pH of the reaction mixture were seen to have considerable effects on the lattice parameters and microstrain of the ZnO nanocrystals, along with their photocatalytic performance. We observed that while the ZnO nanostructures synthesized at very high pH values of the reaction mixture have a high specific surface area, their photocatalytic activity is higher when they are synthesized at acidic pH or pH near the isoelectric point of ZnO. The results demonstrate that the photocatalytic activity of ZnO nanostructures not only depends on their size or specific surface area but also strongly depends on the concentration of catalytic sites at their surface.