The present study investigated photosynthetic rates and their regulation by light within the upper 5 mm of sediment in a tidal area of Niida River in Hachinohe, Japan. Steady-state concentration profiles of O2, NH4+, NO2−, H2S, and pH in the sediment were measured with microelectrodes. Microzonation of O2 respiration, denitrification and SO42− reduction was found in the sediment. When light intensities exceeded 1050 μmol photons/m2/s, net photosynthetic activity was detected in the upper 0.5 mm of the microbial mat colonizing on the sediment surface in the tidal area. In contrast, gross photosynthetic activity was detected in the upper 1.0 mm of the microbial mat at 1900 μmol photons/m2/s. As light intensity increased, the net photosynthetic rate and O2 penetration depth increased. The maximal net photosynthetic rate and O2 penetration depth were 6.1 μmol O2/cm3/h and 2.2 mm, respectively, at 1900 μmol photons/m2/s. Net photosynthetic rates in the microbial mat in the tidal area were lower than in the upstream sediment. The analysis of continuous O2 concentration measurements in different layers of the microbial mat during artificial light–dark cycles demonstrated that the photosynthetic activity response to changes in light intensity was extremely fast (a few seconds) and the O2 concentration in the microbial mat became stable within 200 s. The measurement of physical and chemical parameters in river water revealed that the study site was relatively polluted and sunlight intensity significantly fluctuated temporally. These results suggested that the in situ microbial processes occurring in the sediment fluctuated in accordance with periodic fluctuations in sunlight intensity.