© 2017, The Oceanographic Society of Japan and Springer Japan KK. A superficial sediment layer (SL) is the top 2–3 mm layer of surface sediment that may contribute to high upward nutrient flux. To study the characteristics and the biogeochemical processes in the superficial layer, the seasonal variation in the total phytopigments (chlorophyll a and pheo-pigments), total organic carbon (TOC), and total nitrogen (TN) of the surface sediments in a shallow coastal area, Shido Bay, were measured, and the influence of the superficial sediment layer on nutrient flux at the sediment–water interface was investigated. TOC and TN content were relatively constant for the SL and subsurface layers (0–1 and 1–2 cm) during the study period. In contrast, total phytopigments content was higher in the SL layer than in the subsurface layers. The results of upward nutrient flux experiments showed higher nutrient release within the whole sediment core (SL remaining) than the SL-less (SL removed) core. Moreover, high nutrient fluxes were observed during the high temperature season, indicating that seasonal variation in nutrient flux was regulated by temperature. Moreover, in the low temperature season, the SL seemed to absorb nutrients, probably because of microphytobenthos photosynthesis that took up the nutrients under the sufficient light penetration to the sea floor.