We measured oxygen (O2) fluxes in two major shallow subtidal benthic habitats (kelp bed (KB) and bare rock (BR) covered with crustose coralline algae) of Dokdo islet in the East Sea by applying noninvasive in-situ aquatic eddy covariance (AEC). The AEC device allows time series measurements (~24 h) of three-dimensional velocity (u, v, and w components) and high-resolution dissolved O2. This allows estimation of O2 exchange flux via benthic habitats. Local flow rates and irradiance levels were found to be major factors controlling O2 exchange flux in the rocky habitats. Gross primary production rates tended to be significantly higher in KB (163 mmol O2 m–2 d–1) than in BR (51 mmol O2 m–2 d–1). The net ecosystem metabolisms were assessed as opposite types, with 8 mmol O2 m–2 d–1 in KB (autotrophy) and –12 mmol O2 m–2 d–1 in BR (heterotrophy). Our results indicate that kelp beds are important for organic carbon cycling in rocky coastal waters and that AEC application to macroalgae habitats is a useful assessment approach.