Spatial investigations of pore water nutrient concentrations and their theoretical fluxes were carried out in six different sediment types within a coastal environment (Shido Bay, the Seto Inland Sea, Japan fluxes increased with the C:N ratio of sedimentary organic matter. Differently, the highest Si(OH) 4 fluxes were related with the relative high pheo-pigments and biogenic silica (Bio-Si) contents in the surface sediment, which are affected by fecal matter from the oyster culture. As a result, organic matter availability was found to be an important factor in regulating spatial variability of NH 4 + and PO 4 3− fluxes, whereas significant contents of sedimentary pheo-pigments and Bio-Si characterise the sites where Si(OH) 4 is available.