Mesophotic (low light) sands were studied in Hawaiian coastal waters (39–204 m water depth) from O‘ahu to Kaho‘olawe by sampling inside and outside of extensive macroalgal meadows of chlorophytes Halimeda kanaloana and Udotea sp. during September 2004, December 2004, and November 2006. Porewater nutrient concentrations in these permeable sediments were comparable to those in nearshore sands and were highly elevated at sediment depths available to holdfasts of some algae (5–10 cm); maximum levels were 3.0 µM reactive phosphorus, 33 µM nitrate, 0.70 µM nitrite, 38 µM ammonium, and 130 µM silicic acid. Benthic material is calculated to be the major source of organic matter driving diagenesis in these sediments. Vegetated sediments appeared more oxidizing than unvegetated sediments, and the presence of macroalgae, particularly Halimeda, was generally associated with higher sediment dissolved inorganic carbon levels. Halimeda-vegetated sediments generally had low dissolved inorganic nitrogen (DIN) levels compared to the Udotea-vegetated and non-vegetated sediments, consistent with the net N loss indicated by sediment stoichiometric relationships. In contrast, Udotea-vegetated sediments showed minimal apparent algal DIN uptake.