Climate change is one of the biggest challenges facing humankind. Higher temperatures and changes in precipitation will lead to a greater frequency of drought, wildfire, and intense storms that will threaten systems already vulnerable to climate and anthropogenic change. These threats will transform carbon delivery across the terrestrial–aquatic interface. This study investigated how anthropogenic activities and climate influence organic carbon delivery using Englebright Lake, a reservoir in California, as a model system. Organic carbon accumulation in three depositional settings (bottomset, foreset, topset) was analyzed using fatty acid, sterol and lignin biomarkers and compared to records of watershed events to determine responses to dam construction, mining impacts and flood events. Concentrations of long chain saturated fatty acids, plant sterols, epi-brassicasterol/brassicasterol and lignin biomarkers increased by an order of magnitude in foreset deposits in response to flood events (p < 0.007 for each biomarker). Hydraulic mining for gold was recorded as near-zero concentrations of terrigenous biomarkers in topset deposits, whereas decreases in diacids coincident with increases in aquatic sterols in bottomset deposits reflected the response to dam construction (p < 0.007 for each biomarker). Organic carbon accumulation was controlled by event magnitude and duration, and climate-driven event signals were up to an order of magnitude larger than anthropogenic-driven event signals. These data demonstrate the importance of understanding the depositional environment because the ability to characterize three different depositional settings in Englebright Lake enabled us to identify the smaller anthropogenic signals that would have been obscured by the much larger response to climate events.