Bacterial pathogens of water origin have potential public threats thus suggesting the need of developing efficient and sustainable water disinfection strategies from waterborne pathogens. We set out to synthesize different controlled morphologies of graphitic carbon nitride (g-C3N4) polymer, evaluate their comparative effects on the generation of reactive oxygen species (ROS), and investigate potential applications in water purification systems. Characterization of the synthesized microstructures of g-C3N4, such as melamine-cyanuric acid (MCA)-based rosette-type, rod-type, 2D hexagonal, and 3D cubic mesoporous silica was accomplished using Fourier transform infrared (FT-IR), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), X-ray diffractometry (XRD), and transmission electron microscopy (TEM). The microbial inhibitory potential of 2D gC(3)N(4) photocatalyst against waterborne Escherichia coli, Staphylococcus aureus, and Salmonella typhimurium was evaluated based on the effective activity of 2D g-C3N4 upon visible light excitations. The microbicidal efficiency of 2D g-C3N4 was evident within 30 min of visible light exposure via direct interaction, while other microstructures of g-C3N4 demonstrated only slight antimicrobial effects after 120 min, with insufficient ROS generation. The antimicrobial and ROS-generating effects of 2D g-C3N4 depended on the type and surface area of the synthesized 2D g-C3N4 material. Considering its availability and excellent disinfection activity, 2D g-C3N4 obtained from simple and convenient facile synthesis is a promising solar-driven photocatalyst for clearing microbial contamination from water.