Great strides have recently been made in identifying and characterizing the staggering diversity of microorganisms conducting primary and secondary production, nutrient transformation and mineralization processes that underlie ecosystem and regional biogeochemical, trophodynamic and ecological change. We are now faced with the challenge of assigning and coupling function to structure in highly complex and interactive microbial communities mediating such change. Previous and ongoing ecophysiological work has shown that microbial processes controlled by environmental variables and limiting resources are highly specific in terms of what, when, where and why they are active, not to mention how they impact ecosystem dynamics. As such, it is imperative that we assess the activities and roles of key microbial ‘players’ along the appropriate environmental scales and gradients catalysing ecological change. Here, we discuss conceptual and technical challenges for some key microbially mediated environmental processes, problems and extremes that require synthesizing our growing knowledge of microbial community structure with emerging knowledge of function in aquatic ecosystems. We emphasize the importance of assessing ecological change over a range of relevant time scales that vary from minutes to millennia and spatial scales that range from microscale aggregates to ocean basins.