This article was presented as a position paper during the Environmental Biotechnology and Microbiology Conference in Bologna, Italy in April 2012. It indicates major and emerging environmental biotechnology research and development (R&D) priorities for EU members in the field of sustainable remediation and purification of agro-industrial and municipal wastewater. The identified priorities are: anaerobic/aerobic microbial treatment, combination of photochemical and biological treatment, phytoremediation and algae-based remediation, as well as innovative technologies currently investigated, such as enzyme-based treatment, bioelectrochemical treatment and recovery of nutrients and reuse of cleaned water. State of the art, research needs and prospective development in these domains are crucially discussed. As a result, goals of the future development of bioremediation and purification processes are defined and the way to achieve them is proposed.