Measurements of dissolved inorganic nutrients (NH4+, NO2-+NO3-, HPO4-2 and SiO2) in pore waters (PW) and overlying bottom waters (OBW) were carried out in sediments of two reefs on the Jordanian coast of the Gulf of Aqaba at different water depths down to 30 m. One of the two sites was a marine reserve in front of the Marine Science Station (MSS) and the other hosted an Industrial Complex Zone (ICZ). The PW samples were retrieved using specially designed interstitial water traps. The concentrations in the OBW were within the typical range reported for oligotrophic tropical oceans. They showed minor variations with depth due to a well-mixed water column. Higher nutrient values were found at the ICZ compared to MSS suggested anthropogenic nutrient inputs. Our results showed significantly higher nutrient concentrations in the PW than in the OBW. The average concentrations in PW were about 16, 6, 9 and 5 times higher than the average values reported in the OBW for NH4+, NO2-+NO3-, HPO4-2 and SiO2 respectively. Average fluxes of the dissolved inorganic nutrients were estimated in this study using the pore water gradient concentration across the sediment-water interface. Average diffusion fluxes were in the ranges 1.41-46.44, 2.68-18.25, 0.04-0.60 and 9.68-16.85 mmol m-2 d-1 for NH4+, NO2-+NO3-, HPO4-2 and SiO2 respectively. Flux of all nutrients was higher at the MSS. This can be attributed to higher sediment organic matter content and high biological activity. The results of this study demonstrate (i) the importance of coral reef sediments in recycling nutrients for coral reef communities and (ii) the effect of pumping cooling water on the nutrient regeneration process.