The relationship between carbon burial and sedimentation in reservoirs is unknown, contributing to uncertainty in our understanding of the net impact of dams to the global carbon budget and exposing gaps in our fundamental understanding of the transport, processing, and deposition of organic matter in fluvial and lacustrine systems. Taking opportunistic advantage of the removal of two high‐head dams, we investigate this relationship by developing a stratigraphic, process‐based framework to estimate total carbon accumulation as a function of depositional environment in the sediments of two former ~1‐km2 reservoirs on the Elwha River, Washington, USA. Former Lake Mills (upstream; completed 1927) accumulated ~330 Gg, with depositional zone average accumulation rates from 229 to 9,262 gCm2/ year, while Former Lake Aldwell (downstream; completed 1913) accumulated ~91 Gg (263 to 2,414 gCm2/ year). Carbon storage in both reservoirs was dominated by heterogeneous, coarse organic matter and woody debris in the coarse‐grained delta slope and relatively coarse‐grained prodelta regions of the reservoirs, with little in the gravel‐dominated, subaerial delta plains. Carbon accumulation in fine‐grained lacustrine and prodelta sediments was relatively homogeneous, but turbidity flows from the Gilbert‐style delta slope in former Lake Mills delivered significantly more carbon to the prodelta than the mouth bar‐style delta of former Lake Aldwell. C:N ratios support interpretation of most organic matter in both reservoirs as allochthonous. Sampling schemes based only on lacustrine and/or prodelta would underestimate total carbon accumulation by up to 30% in former Lake Aldwell but overestimate carbon by up to 47% in former Lake Mills.