Benthic chamber measurements of the reactants and products involved with biogenic matter diagenesis (oxygen, ammonium, nitrate, silicate, phosphate, TCO2, alkalinity) were used to define fluxes of these solutes into and out of the sediments off southern and central California. Onshore to offshore transects indicate many similarities in benthic fluxes between these regions. The pattern of benthic organic carbon oxidation as a function of water depth, combined with published sediment trap records, suggest that the supply of organic carbon from vertical rain can just meet the sedimentary carbon oxidation + burial demand for the central California region between the depths 100–3500 m. However, there is not enough organic carbon raining through the upper water column to support its oxidation and burial in the basins off southern California. Lateral transport and focusing of refractory carbon within these basins is proposed to account for the carbon buried. The organic carbon burial efficiency is greater off southern California (40–60%) compared to central California (2–20%), even though carbon rain rates are comparable. Oxygen uptake rates are not sensitive to bottom water oxygen concentrations nor to the bulk wt. % organic carbon in surficial sediments. Nitrate uptake rates are well defined by the depth of oxygen penetration into the sediments and the overlying water column nitrate concentration. Nitrate uptake accounts for about 50% of the total denitrification taking place in shelf sediments and denitrification (0.1–1.0 mmolN/m2d) occurs throughout the entire study region. The ratio of carbon oxidized to opal dissolved on the sea floor is constant (0.8 ± 0.2) through a wide range of depths, supporting the hypothesis that opal dissolution kinetics may be dominated by a highly reactive phase. Sea floor carbonate dissolution is negligible within the oxygen minimum zone and reaches maximal rates just above and below this zone (0.2–2.0 mmol/m2d).