Depositional and diagenetic controls on the distributions of carbon, sulfur, and iron (C-S-Fe) in modern sediments and upper Pleistocene mudrocks of the Eel River Basin (ERB), northern California continental margin, were investigated using a combination of geochemical, radioisotopic, and sedimentological methods. A mass balance based on down-core profiles of porewater and solid-phase constituents and diagenetic modeling suggests that only 12-30% of the pyrite-S produced via SO4-2 reduction during burial is retained in modern shelf and upper slope deposits of the ERB. Bioturbational reoxidation of initially reduced S is inferred to be the major control on S preservation, on the basis of an observed inverse relationship between pyrite-S retention and biological mixing intensity, estimated from profiles of excess 234Th. Importantly, these findings argue that massive depositional episodes on the shelf following floods of the Eel River have a negligible long-term impact on bioturbating macrofauna and the potential to affect geochemical properties of the sediments. Down-core profiles of reactive Fe3+ and Py-Fe(II) for the modern deposits suggest that highly reactive Fe phases are sulfidized well within ∼ 500-2000 years of burial, thereby limiting later pyritization, which could occur through sulfidation of less reactive phases. This result explains the low (≤ 0.4) degree of pyritization (DOP) values exhibited by both modern and ancient deposits of the ERB and lends support to the notion that pyritization in aerobic continental-margin sediments is largely associated with highly reactive detrital Fe oxides. Comparable mean C/S weight ratios for modern sediments (5.4 ± 3.3, 1σ) and mudrocks (6.9 ± 4.5) of the ERB suggest that the upper Pleistocene strata reflect a geochemical environment analogous to that of the modern margin. Specifically, the C-S-Fe signatures shared by the modern and ancient deposits are a consequence of similar detrital Fe mineralogies, initial organic-matter content (Corg ≤ 1%) and composition (C/N = 13 to 17, δ13Corg = -22 to -25‰), burial rate, and importantly, bioturbation intensity. The findings of this study have important implications for the use of C-S-Fe signatures as indicators of diagenetic processes in dynamic, continental-margin environments.