Several studies highlighted the occurrence of circular pools in intertidal flats of different coastal systems and their transient water chemistry over both tidal and diurnal cycles. However, little is known about (1) the response of benthic biogeochemical reactions and fluxes at the sediment-water interface over such short time scales, and (2) the role of these tidal pools in the biogeochemical functioning of coastal systems. Based on in situ microprofiles and water sampling, we investigated the dynamics of dissolved oxygen (O2), nutrients, sulfides and metals, and the associated fluxes at the sediment-water interface in tidal pools from the Arcachon Bay (Atlantic coast of France). Our integrative approach included several tidal and diurnal cycles over two different seasons in the presence and absence of Zostera noltei. The results show that water temperature and light irradiance were the main factors driving the biogeochemical functioning of the tidal pools, as they controlled the physiological activity of the microphytobenthos. Changes in light radiations induced diurnal fluctuations of O2 concentrations within surficial sediment, thus resulting in fluctuations of the O2 diffusive fluxes at the sediment-water interface and of the O2 penetration depth in sediment. At high tide, the increase in turbulence above the sediment induced the advection of oxygenated water within the first millimeters of sediment, resulting in a significant increase in porewater O2 concentrations and sediment O2 penetration depth. Porewater sulfide concentrations and apparition depth were concomitant with the O2 dynamic over both diurnal and tidal cycles, indicating that intermediate redox diagenetic processes were impacted by O2 dynamic over such short time-scale. The rapid changes in redox processes in the sediment column are confirmed by a significant flux of dissolved manganese toward the water column during nighttime. The consumption of nitrate and the release of ammonium and phosphate, associated to the mineralization of the organic matter in the surface sediment did not appeared related however to such short time cycles. The efflux of dissolved silica from the sediment was most likely associated with the enhanced dissolution of Si-bearing particles in surface sediment at higher temperatures, although silica uptake by Z. noltei was also noted. This study clearly shows that tidal pools function as natural incubators of transient biogeochemical processes. A rough assessment of the nutrient budget at the scale of the bay indicates the tidal pools may contribute significantly to the biogeochemical functioning of Arcachon Bay.