The role of diversity in ecosystem processes has been hotly debated because the stakes are high. On one hand, if only a small subset of species is central to maintaining ecological stability, then nature-based solutions and restoration programs will be easier to design. On the other hand, deeming a species “unimportant” under a specific set of circumstances does not preclude its importance in a yet to be studied context. Diversity breeds redundancy and stability, but it is difficult to determine thresholds of species loss required to maintain stability. Microbiomes are model ecosystems for testing theories about the importance of diversity. Microbiomes frequently include thousands of species, spanning the tree of life, that can be manipulated and observed at small spatial and temporal scales. Quantitative stable isotope probing (qSIP) integrates stable isotope tracers with omics to measure the activity rates of species in intact field samples. Across multiple datasets (algae, fungi, and bacteria), in rivers and soils, we explore how diversity at multiple levels, ranging from phylogenetic and functional diversity to species richness and evenness, regulates ecological processes including photosynthesis, n-fixation, decomposition and redox reactions. Results suggest that at any given time, biogeochemical processes can be dominated by a small fraction of the microbial diversity present. Temporal trends, however, reveal that the suite of species driving ecological processes change seasonally. Experimental manipulations of temperature, nutrients, and carbon inputs indicate that unique suites of species are activated under different environmental conditions. Like in macro-ecosystems, some microbial species are functionally more important than others. Terminology identifying important roles in ecosystems such as keystone or foundation species are becoming applicable to microbiomes. I will discuss how people might include microbial diversity and microbiome research into water management.