The Special Issue "Technological Eco-Innovations for the Quality Control and the Decontamination of Polluted Waters and Soils" deals with the most recent research activities carried out at lab and field scale on eco-sustainable tools for the remediation of contaminated environmental substrates. It is particularly devoted to highlight the relevance of biological organisms (plants, microbes, algae) to assess the chemical contamination in water and soil and to remediate such matrices from the pollution caused by the human activities. Therefore, bioremediation is a primary focus of most of the articles published within the present Special Issue. Bioremediation is a promising environmentally friendly technology to deal with the chemical pollution in different ecosystem compartments and its integration with the traditional approaches might represent a significant breakthrough for the environmental decontamination. An overview of the potential of the eco-innovative technologies, with nature-based solutions associated with the modern analytical techniques, is offered along the contributions forming the Special Issue. In this volume, different contaminants occurring in various environmental matrices are focused, both in controlled conditions and on site, with many interesting outcomes useful from research perspectives.