The Green River Formation of Utah, Colorado, and Wyoming represents a ~10 million-year early-middle Eocene record of an unusually large, productive lacustrine system composed of several interconnected basins. This system gave rise to one of the largest oil shale deposits in the world, which preserves a rich trove of information about the climate and ecosystems that prevailed during the Early Eocene Climatic Optimum. This study uses multiple analytical approaches, including both traditional methods and novel proxies, to determine what brought about the accumulation of the unusually-rich oil shales (>40% TOC) of the Mahogany Zone in the Uinta Basin portion of the Green River Formation. The organic-rich mudstones of the Mahogany Zone exhibit strong micro-scale heterogeneity, indicating complex controls on organic matter production and distribution. Petrographic observations indicate highly variable amounts of terrestrial organic matter (spores, wood and plant debris), with the most abundant being amorphous organic material in thin organic-rich laminae. Biomarker ratios indicate that the organic-rich laminae consist of different types of microbially derived organic matter, primarily bituminite and organo-minerallic aggregates of the fluorescent liptinite group. These largely lacustrine-derived laminated deposits are argued to have been produced by large intrato inter-annual algal blooms and other enhanced microbial productivity events paced by longer-term sub-orbital cycle fluctuations, such as El Niño–Southern Oscillation or sunspot variations. The Mahogany Zone deposits appear to have sequestered enough carbon (~64.25 Gt estimated) to suggest that, in aggregate, they were large enough to cause a draw-down of terrestrial CO2 and exert a significant negative feedback effect on climatic warming. During the climatic cooling that occurred on the declining limb of the Early Eocene Climatic Optimum, the sedimentary provenance in the Uinta Basin shifted from southerly sources dominated by large ephemeral fluvial systems, to northerly sources rich in feldspathic and carbonate detritus derived from northern sites in Wyoming. The latter were delivered to the Uinta Basin via a network of interconnected lacustrine basins. Increasing volcaniclastic material delivered from these northerly basins infilled the Uinta Basin from east to west, and their arrival heralded the end of organic-rich deposition, most notably the prolific oil shales for which the Green River Formation is renowned.