Here we report multiple parameters used to describe the diagenetic state of sediments, including total hydrolyzable amino acid (THAA), amino acid enantiomer, chlorin (CI) and amino acid degradation (DI, RI) indices, along a transect between the Upper St. Lawrence Estuary and the Gulf of St. Lawrence, Canada. The study area is characterized by gradients in water oxygen concentration, water depth, organic matter (OM) source, primary productivity, and sedimentation rate. Both CI and DI indicate a decline in OM reactivity, with the transition from a more terrestrial to a more marine-dominated sedimentation regime as one moves from the shallow Upper Estuary (23–95 m) to the hypoxic, mid-depth Lower Estuary and to the deep (>400 m), well-oxygenated Gulf. Whereas the CI more accurately reflected OM reactivity in surface sediments and sediments down to 5 cm, the amino acid-based degradation indices (DI and RI) better described degradation in sediments down to 35 cm. Systematic variations in the amino acid composition along the Laurentian Channel confirmed the increased diagenesis of OM with distance from the Upper St. Lawrence Estuary. The ratio of d/l-stereoisomers of alanine increased along the transect, and the co-variation between DI and the d/l-Ala suggest a close coupling between the extent of diagenesis and the accumulation and selective preservation of bacterially-derived cell wall material in the sediments. The same patterns that we observed along the estuarine transect were present down-core in two sediment cores, confirming the robustness of our reactivity indices. Oxygen exposure time of the sediments appears to strongly determine sediment OM reactivity in the St. Lawrence Estuary. The sediment oxygen regime itself is related to the interplay between water column depth, vertical OM flux, and reactivity of settling OM.