This special issue of the Groundwater for Sustainable Development “Contaminant Transport and Fate in Freshwater Systems – Integrating the fields of geochemistry, geomorphology and nanotechnology” provides an update of the current knowledge on the sources, pathways, and movement of anthropogenic and geogenic contaminants in the environment, the holistic interactions between biotic and abiotic components of the ecosystem, and the avant-garde technologies as innovative strategies for environmental management. We aims to provide a future platform for interaction and collaborative efforts between different workers in the scientific field. As this issue highlights the three keywords: hydro-geochemistry, geomorphology and nanotechnology; therefore, it will facilitate a unique amalgamation of pure as well as applied scientific ideas. Therefore, this combined effort will be much more beneficial and will lead to great developments in the near future. This will result in a better understanding of the background processes and the factors controlling the contamination process and therefore contribute to the development of more efficient and sustainable technologies and management options. This issue also has the broader purposes to influence the policymakers which in turn may lead to greater investments and research grants in the fields covered by the said volume, which can ultimately lead to more quality research in these fields.