While marine seagrass habitats are acknowledged as sinks for carbon and nutrients, much less is known about sequestration in brackish-water vegetation. Here, we quantify the amount of organic carbon (C_org) and total nitrogen (TN) in shallow bay sediments (0–25 cm) in the brackish Baltic Sea and assess how it varies with morphometric isolation from the sea, catchment characteristics and abundance of brackish-water vegetation. The sedimentary C_org and TN content per surface area varied across the bay isolation gradient (mean C_org: 2500–4600 g/m²; mean TN: 320–570 g/m²), with enclosed bays having the highest percentage content of C_org and TN, but low sediment density (< 0.1 g cm³), while open bays had more compact sediment with lower percentage content of C_org and TN. The influence of catchment and vegetation characteristics on the sediment C_org and TN content was less clear, suggesting that coastal morphology affecting hydrodynamic exposure is an important determinant of C and TN accumulation in brackish-water bays. The results show that morphometrically isolated shallow coastal areas constitute significant sinks for carbon and nitrogen, which should be considered in management and in any regional estimates of blue carbon and nutrient sequestration functions.