In order to investigate the influence of sediment physical and chemical characteristics on the degradation of deposited organic matter, decomposition in three sediments from the Gulf of Aqaba (Red Sea) that differ in permeability and mineral composition were compared. Freeze-dried Spirulina was added to coarse carbonate and silicate sands from a shallow nearshore region and silt-clay sediment from the deeper center region of the Gulf incubated in laboratory chambers. The stirring in the chambers caused higher solute exchange in the coarse permeable sands relative to the fine less permeable silt due to the generation of advective fluid exchange between the sediment and overlying water. This enhanced exchange increased the decomposition rates of organic matter in the incubated sands. The decomposition rates of total organic carbon in the permeable carbonate (3.0 mg C m −2 d −1) and silicate sands (2.0 mg C m −2 d −1) exceeded that in the fine-grained sediment (1.4 mg C m −2 d −1). Oxygen consumption in the coarse sands was 3-fold higher than in the silt-clay sediment, with highest rates in the carbonate sand. In carbonate and silicate sands of the same grain size, the carbonate sediment was more permeable than the silicate, resulting in 1.4-fold higher fluid exchange rates and 1.4-fold larger sedimentary organic matter mineralization rates. An in situ experiment comparing trapping efficiencies in carbonate and silicate sands showed that the higher fluid exchange rate in the carbonate sand results in larger filtration rates and a faster accumulation of particulate organic matter from the boundary layer. These experiments demonstrate that with respect to sedimentary mineralization rates, higher transport rates in permeable coarse sediments can outweigh the effect of a higher specific surface area in fine-grained silt sediments. In permeable sands, however, the higher specific surface area and fluid exchange in biogenic carbonate sands result in higher mineralization rates than in silicate sands of the same grain size.