Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Within a broad ecological framework, we conceptualize the spatio-temporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic foodwebs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. To date, aquatic fungi and their interactions have largely remained "hidden" and require interdisciplinary efforts to be explored in an ecosystem context. There remain obvious methodological and knowledge gaps to explore potential functions of aquatic fungi, moving from the microscale to the global scale. This knowledge is urgently needed since we humans strongly interfere with structure and function of natural ecosystems by permanently reshaping most of the Earth's surface and creating vast areas of novel urban habitats. Introduction: Recent advances in DNA sequencing technology have revealed that fungi are abundant in many, if not all aquatic ecosystems, however their diversity, quantitative abundance, ecological function and, in particular, their interactions with other microorganisms, remain largely speculative, unexplored and missing from current general concepts in aquatic ecology and biogeochemistry 1-4. This is surprising since terrestrial-focused research has understood the outstanding ecological role of fungi for >100 years, and therefore fungi constitute a major component of general concepts in terrestrial science 5,6. In aquatic ecosystems, the systematic analysis of fungal diversity and their ecological roles has faced several setbacks due to methodological limitations and a too small scientific community, in particular in the marine environment 7-11. This review focusses on aquatic fungi, which form a morphologically, phylogenetically, and ecologically diverse group 7. We here broadly define "aquatic fungi" as fungi that rely for the whole or part of their life cycle on aquatic habitats (FIG. 1). Three groups (indwellers, periodic immigrants and versatile immigrants) based on their degree of adaptation and dependence on aquatic habitats have been previously defined 12. We highlight the numerous knowledge gaps in their diversity, interactions and functional roles, as well as methodological limitations. In this review we propose new research avenues to set aquatic fungi in a broad ecological framework. Here, we do not explore the many existing gaps in the fungal phylogenetic tree. In aquatic systems, fungi constitute a significant proportion of eukaryo...