The demand for clean water is rising due to factors such as population growth, urbanization, and rapid industrialization. Simultaneously, concerns regarding the health implications of water pollution on humans, wildlife, and plants are also on the rise. The utilization of nanobiotechnology-based techniques shows great potential in addressing the issue of contaminated water systems and improving the efficiency of water treatment processes. This chapter has explored the undeniable role of novel and efficient nanobiotechnologies in achieving SDG 6, i.e., targeting clean water and sanitation. Furthermore, the application of these techniques in the removal of heavy metals, dyes, pesticides, and pathogens to ensure clean water and sanitation are discussed. The chapter has also shed light on the opportunities and challenges that lie ahead for the widespread implementation of nanobiotechnologies in industrial settings.