This Special Issue of Physics and Chemistry of the Earth presents 33 papers drawn from the 12th WaterNet/WARFSA/GWP-SA annual symposium held in Maputo, Mozambique between 26 and 28 October 2011. It is the 11th special issue in the WaterNet series. About 220 presentations were made orally or in poster form under the main symposium themes as well as in various parallel sessions that were conducted to discuss topical issues. Of these papers 78 were eventually submitted for review and publication in this issue out of which only 42% of the submitted papers appear in this Special Issue. This issue has not digressed from the traditional format of presenting papers according to themes. The main symposium themes were Hydrology, Water and Environment, Water and Land, Water Resources Management, Water and Society, and Water Supply and Sanitation. The majority of the accepted papers fall into the themes of Water and Environment, Hydrology and Water Supply and Sanitation. This statistic may be an indicator of the thrust in regional research where more attention is being paid to hydrological issues as well as water supply, sanitation and environmental considerations from an IWRM perspective. This is true to a large extent given the challenges of water scarcity, climate change and pollution throughout the sub-Saharan region where communities are demanding more up-to-date solutions to cope with these daily challenges. The large number of presentations and submissions from young scientists is also encouraging as this is evidence of the success in capacity building in the water sector where young professionals are being encouraged to share their research findings with the wider scientific community. Highlights of the research published in this special issue are presented in section below.