Abstract Eutrophication is one of the most significant ecological problems in large-river delta-front estuaries (LDEs) around the world. We used TOC, TN, δ13C, δ15N and three stable sedimentary chloropigments (pyropheophytin-a [pPHtin-a], sterol chlorin esters [SCEs] and carotenol chlorin esters [CCEs]) as geochemical proxies to examine historical trends of eutrophication over the last few decades in the Changjiang and Mississippi LDEs. Concentrations of sedimentary pPHtin-a, SCEs and CCEs increased from 15, 12 and 120nmolg−1 OC in 1960s to 51, 32 and 256nmolg−1 OC in 1990s on the inner shelf of the East China Sea, respectively, and from 57, 69 and 31nmolg−1 OC in 1950s to 70, 90 and 44nmolg−1 OC in 2000s in the Mississippi Canyon, respectively. Riverine loading of DIN flux to LDE increased from (261±109)×106kgyr−1 in pre-1980 to (1385±209)×106kgyr−1 in post-1990 in the Changjiang LDE, while nitrate flux increased from (322±89)×106kgyr−1 in the 1950s to 1960s to (589±123)×106kgyr−1 in the 1970s, and DIN flux kept relatively stable in (963±250)×106kgyr−1 from the 1980s to 2000s in the Mississippi LDE. This work reveals that the stable sedimentary chloropigments in accumulating sediments on the inner shelf are suitable biomarkers for examining past changes in eutrophication in the Changjiang and Mississippi LDE ecosystems. The historical record of riverine nutrient inputs as related to changes in the watershed (e.g., fertilizers and manure) is well-correlated with down-core concentrations of stable pheopigment biomarkers in sediments at both LDEs. These results support the coupling between enhanced phytoplankton abundance and increasing anthropogenic nutrients input to the inner shelves of these LDEs.