The main questions in evolutionary ecology have been summarized by “Why is what where?”. Investigating these topics in aquatic fungi is difficult because of their small and indeterminate bodies (thalli). Major advances in the last 20 years have been due to the wide-spread use of molecular methods, primarily based on amplification and characterization of DNA and RNA sequences. Beginning with DGGE and T-RFLP and culminating in NGS (HTS), they have greatly increased our knowledge of fungal taxonomic diversity, biogeography and metabolic potential. Attempts to use these data to interpret fine-scale organization of fungal communities have been less successful. Similar difficulties arise when trying to use molecular data to characterize and predict large-scale ecosystem processes. The metabolic theory of ecology (MTE) posits that the metabolic rate of organisms governs most patterns in ecology. It is based on predictable relationships between body size, temperature and metabolic rate across all organisms. There have been very few attempts to connect body size and metabolic rate in fungi (none in freshwater fungi), but several recent global studies have attempted to estimate temperature sensitivity of the rate of leaf decomposition, which is a fundamental ecological process in streams. One underlying objective is the ability to predict how these ecosystems will react to anthropogenic changes, such as global warming. No simple, unequivocal conclusions have emerged; the local context often has a major impact. A potentially dominant influence is the phylogenetic (evolutionary) history of investigated plant species.