The recent application of sophisticated instrumentation and novel experimental techniques to environmental systems has driven the study of natural nanoparticles and nanoparticle systems towards new horizons. Moving beyond the detection of engineered nanoparticles in natural systems, these technologies create new knowledge about the composition, behaviour, and functions of natural nanoparticles as individual entities and particle systems. In this perspective article, we describe the progress and frontiers in this research area using case studies drawn from a range of published and unpublished data spanning diverse environmental systems. The companion paper Exploring environmental nanobiogeochemistry using field-flow fractionation and ICP-MS-based tools: background and fundamentals defines the emerging field of environmental nanobiogeochemistry and describes the fundamentals, optimization, advantages, and disadvantages of field-flow fractionation and ICP-MS-based techniques for advancing our understanding of natural nanoscale particles and particle systems. Thus, by combining the necessary background with the most recent findings and key challenges, these contributions provide key knowledge for new and established researchers entering this exciting field and lay the groundwork for future research.