Abstract Magnesium concentrations in deep-sea sediment pore-fluids typically decrease down core due to net precipitation of dolomite or clay minerals in the sediments or underlying crust. To better characterize and differentiate these processes, we have measured magnesium isotopes in pore-fluids and sediment samples from Ocean Drilling Program sites (1082, 1086, 1012, 984, 1219, and 925) that span a range of oceanographic settings. At all sites, magnesium concentrations decrease with depth. At sites where diagenetic reactions are dominated by the respiration of organic carbon, pore-fluid δ 26Mg values increase with depth by as much as 2‰. Because carbonates preferentially incorporate 24Mg (low δ 26Mg), the increase in pore-fluid δ 26Mg values at these sites is consistent with the removal of magnesium in Mg-carbonate (dolomite). In contrast, at sites where the respiration of organic carbon is not important and/or weatherable minerals are abundant, pore-fluid δ 26Mg values decrease with depth by up to 2‰. The decline in pore-fluid δ 26Mg at these sites is consistent with a magnesium sink that is isotopically enriched relative to the pore-fluid. The identity of this enriched magnesium sink is likely clay minerals. Using a simple 1D diffusion–advection–reaction model of pore-fluid magnesium, we estimate rates of net magnesium uptake/removal and associated net magnesium isotope fractionation factors for sources and sinks at all sites. Independent estimates of magnesium isotope fractionation during dolomite precipitation from measured δ 26Mg values of dolomite samples from sites 1082 and 1012 are very similar to modeled net fractionation factors at these sites, suggesting that local exchange of magnesium between sediment and pore-fluid at these sites can be neglected. Our results indicate that the magnesium incorporated in dolomite is 2.0–2.7‰ depleted in δ 26Mg relative to the precipitating fluid. Assuming local exchange of magnesium is minor at the rest of the studied sites, our results suggest that magnesium incorporated into clay minerals is enriched in δ 26Mg by 0‰ to +1.25‰ relative to the precipitating fluid. This work demonstrates the utility of magnesium isotopes as a tracer for magnesium sources/sinks in low-temperature aqueous systems.