The Joint Programming Initiative “Water Challenges for a Changing World” (the Water JPI) is an intergovernmental initiative aiming at strengthening European leadership and competitiveness in the field of water research and innovation whilst safeguarding water resources. The Water JPI is harmonizing and mobilizing National and Regional Research, Development and Innovation (RDI) Programmes. This Pilot Call for proposals aims to enable multi-national, collaborative research, development and innovation projects addressing the topic “Emerging water contaminants – anthropogenic pollutants and pathogens”. This call theme is framed within the priority theme “Developing Safe Water Systems for the Citizens”, as described in the Strategic Research and Innovation Agenda (SRIA) of the Water JPI. The overarching aim of this Pilot Call of the Water JPI is to identify new ways to efficiently assess, prevent, control and remove emerging pollutants and pathogens and thereby prevent human health risks and secure ecological functions of water ecosystems now and in the future. The call also intends to stimulate mobility of researchers between participating countries, consequently enhancing European collaborative research during the project life and beyond.