Organic carbon (OC) burial rates in northern lakes are estimated to have increased by 2–3 fold over the past 150 years. However, assessing OC burial efficiency is challenging because (a) long-term (decadal) process are difficult to study in situ, and (b) sediment organic matter (OM) consists of thousands of different compounds from both terrestrial and aquatic sources, which are subject to different degrees of degradation, transformation, or preservation. Here, we used pyrolysis–gas chromatography/mass spectrometry to track changes in the organic molecular composition of individual varve years in a series of sediment freeze cores collected during 1979–2010, allowing us to assess diagenetic changes over ≤31 years (or 12.5 cm depth). As predicted from previous work, the greatest losses over time/depth (18–19 years; 8.5 cm) are for compounds indicative of fresh OM, both terrestrial (e.g., levosugars with 58%–77% lost) and particularly aquatic origin (e.g., phytadiene and phytene amongst chlorophylls with 40%–82% lost). This high variability in degradation of specific compounds has implications for interpreting past changes in C and N. Although OM composition changes only slightly beyond 20 years (8.5 cm), the chlorophyll:lignin ratio (fresh vs. degraded compounds) continues to decline to 31 years (12.5 cm) and is predicted to continue up to 100 years (37 cm depth). In most northern lakes, indications of OM degradation to these depths correspond to sediment ages of 50 to >150 years, suggesting that much of the recent increase in OC burial in northern lakes does not represent permanent sequestration of C.