Anthropogenic pollution coming from industrial processes, agricultural practices and consumer products, results in the release of toxic substances into rural and urban environments. Once released, these chemicals migrate through the atmosphere and water, and find their way into matrices such as sediments and groundwaters, thus making large areas potentially uninhabitable. Common pollutants, including heavy metal(loid)s, radionuclides, aliphatic hydrocarbons and halogenated organics, are known to adversely affect physiological systems in animal species. Pollution can be cleaned up using techniques such as coagulation, reverse osmosis, oxidation and biological methods, among others. The use of nanoparticles (NPs) extends the range of available technologies and offers particular benefits, not only by degrading, transforming and immobilizing contaminants, but also by reaching inaccessible areas and promoting biotic degradation. The development of NPs is understandably heralded as an environmentally beneficial technology; however, it is only now that the ecological risks associated with their use are being evaluated. This review presents recent developments in the use of engineered NPs for the in situ remediation of two paramount environmental matrices: soils and groundwaters. Emphasis will be placed on (i) the successful applications of nano-objects for environmental cleanup, (ii) the potential safety implications caused by the challenging requirements of [high reactivity toward pollutants] vs. [none reactivity toward biota], with a thorough view on their transport and evolution in the matrix, and (iii) the perspectives on scientific and regulatory challenges. To this end, the most promising nanomaterials will be considered, including nanoscale zerovalent iron, nano-oxides and carbonaceous materials. The purpose of the present review is to give an overview of the development of nanoremediators since they appeared in the 2000s, from their chemical modifications, mechanism of action and environmental behavior to an understanding of the problematics (technical limitations, economic constraints and institutional precautionary approaches) that will drive their future full-scale applications.