Microorganisms control the flux of energy, stored as organic matter, into the ocean through the cumulative effects of individual metabolisms and community interactions. Metabolites are the currency of microbial metabolism, are carefully regulated to meet the metabolic demands of organisms living in dynamic environments, and reflect cellular status and metabolic strategies for nutrient acquisition, energy storage, redox maintenance, and more. This dissertation focuses on developing metabolomics techniques for the marine environment and using them to study microbial dynamics over time and space to identify compounds that are key microbial currencies. In order to study natural populations of marine microbes, I developed a method for targeted and untargeted metabolomics data acquisition and analysis with the unique challenges of marine samples in mind (Chapter 2). I use this method to study the influence of the diel cycle on the marine microbial community at Station ALOHA in the North Pacific Subtropical Gyre, ultimately showing synchrony of daytime anabolism and nighttime catabolism as seen through diel oscillations of ubiquitous metabolites including cofactors and vitamins. Through pairing metabolite and gene expression data, I demonstrate the strategies that specific photoautotrophs use to manage the daily fluctuations in solar energy (Chapter 3). To examine how microorganisms respond to other environmental forcings, I investigate the metabolism of microbial communities across the North Pacific Transition Zone and identify metabolic currencies used by those communities to adapt to varying nutrient supply (Chapter 4). Nutrient amendment experiments show the dominance of nitrogen limitation throughout this region and the potential for iron-nitrogen co-limitation near the subtropical chlorophyll front. Finally, in order to explore the potential for metabolites to be nutrient sources to the microbial community, I investigate the ability of natural microbial communities to use the abundant osmolyte glycine betaine. I determine the kinetics of uptake and identify the metabolic uses of glycine betaine in two different natural microbial communities and show that its use as a nutrient differs depending on DIN availability (Chapter 5). In full, this dissertation provides some of the first metabolomics measurements in the natural marine environment and identifies and explores the roles of key organic molecules in shaping the microbial community structure and function.