Oxygen and carbon stable-isotope compositions of modern benthic foraminifera in the Kara and Pechora estuarine regions of the Arctic continental shelf were compared with water δ¹⁸O, δ¹³C_DIC, temperature, and salinity. The foraminiferal δ¹⁸O distribution is mostly similar to that of equilibrium calcite, primarily controlled by mixing of runoff and seawater in near-estuarine areas (depth < 15–20 m), with additional temperature control seaward. The δ¹³C composition is controlled by remineralization of organic matter, mostly imported by rivers, and by water mixing. Most analyses used the common Arctic foraminifer Elphidium excavatum forma clavata, which yields depleted δ¹³C, as expected for an infaunal species. Isotope records for sediment cores off the Pechora and Yenisey rivers show a decelerating rise in isotope values, of up to 10‰ in δ¹⁸O, over the last 10 kyr in a pattern similar to that of rising sea level and concomitant retreat of river mouths, with local complexities probably resulting from glacio-isostatic rebound and changes in sedimentation.