The Conferences on Sustainable Development of Energy, Water and Environment Systems (SDEWES) at the beginning of the 21st century have become a significant venue for researchers to meet, and initiate, discuss, share, and disseminate new ideas in various disciplines of sustainable development. In 2002, the first conference was organised in Dubrovnik, Croatia and since then, 10 more successful conferences were realised. Following the success of international conferences in Dubrovnik, the organizing committees decided to organize the main conference and regional conferences all over the world in even years. In 2016, the second regional SDEWES conference, namely the 2nd South East European Conference on Sustainable Development of Energy, Water and Environment Systems, was held June 15-18 in Piran/Portorose, Slovenia while the 11th SDEWES conference was organised in Lisbon, Portugal on September 4-8. There were 10 special sessions dedicated to various sustain ability topics organised in both conferences. This special issue is based primarily upon a collection of 35 papers selected from among 538 scientific contributions presented at the 2nd SEE and 11th SDEWES Conferences. Moreover, this editorial summarises SDEWES published articles that have addressed and identified problems or provided the background for the research that is reported in the current special issue. The main topics of the selected papers address sustainable combustion technologies, renewable energy sources and sector integration, including the integration of renewable technologies in the urban environment, the integration of heat, cold, electricity and fuel production in buildings and industrial applications, heat exchangers and heat exchanger networks, the development and integration of energy storage for concentrated solar power plants, and sectorial integration of bioenergy resources and biorefineries with a particular focus on system integration for efficient and low-carbon systems.