According to embodiments of the invention, a selective ultraviolet disinfection method is provided. The method includes selecting operating parameters for an ultraviolet disinfection process of flowing liquid carrying first and second types of entities to affect the first type of entities while the second type of entities remains intact, illuminating the liquid with ultraviolet light according to the operating parameters and continuously adjusting the operating parameters based on real-time measurements of ultraviolet transmission and flow rate of the liquid.