Integrating microalgae systems (MAS) at municipal wastewater treatment plants (WWTPs) to produce of bioenergy offers many potential synergies. Improved energy balances provide a strong incentive for WWTPs to integrate MAS, but it is crucial that WWTPs maintain their barrier function to protect water resources. We perform a prospective analysis of energy and emission balances of a WWTP with integrated MAS, based on a substance flow analysis of the elements carbon (C), nitrogen (N), and phosphorus (P). These elements are the main ingredients of wastewater, and the key nutrients for algae growth. We propose a process design which relies solely on resources from wastewater with no external input of water, fertilizer or CO(2). The whole process chain, from cultivation to production of bioelectricity, takes place at the WWTP. Our results show that MAS can considerably improve energy balances of WWTPs without any external resource input. With optimistic assumptions, they can turn WWTPs into net energy producers. While intensive C recycling in MAS considerably improves the energy balance, we show that it also impacts on effluent quality. We discuss the importance of nonharvested biomass for effluent quality and highlight harvesting efficiency as key factor for energy and emission balances of MAS at WWTP.