The potential microbial risk from using treated wastewater is a burning issue to be studied. In Sweden, only a small part of treated wastewater is reused directly, although water reuse could be beneficial. Disinfection is virtually never practised and no protective guidelines for water reuse are found in Sweden. Based on a 1 year monitoring programme of water quality, this paper estimates the microbial risk of Escherichia coli and rotavirus in treated wastewater for different applications of irrigation, landscape, industry, unban non-potable water. A Quantitative Microbial Risk Assessment model is used and the samples were collected from the pond system of Källby wastewater treatment plant in Lund, Sweden. The results are used to evaluate if the treated wastewater after tertiary treatment process combined with pond system can be reused for different applications from a microbial point of view. The risk assessment results show that the studied water is only suitable for agriculture irrigation, while additional treatment or disinfection are needed for other applications since the potential risks are higher than the value that can be accepted. The protective guidelines are discussed based on the process and results of risk assessment and suggestions for establishing a structure of guidelines in Sweden are presented.