To understand the characteristics of sedimentary and benthic environments in habitats of naturally-occurring intertidal benthic macroalgae, various geochemical parameters of sediment (grain size, ignition loss [IL], chemical oxygen demand [COD], and acid volatile sulfur [AVS]) and pore water (temperature, salinity, pH, and nutrients) were measured in the southern intertidal zone of Hampyeong Bay at two month intervals from April to October 2009. Ecological characteristics including the distribution and biomass of benthic macroalgae were also investigated. Benthic macroalgae were distributed below 4 to 5 m depth from mean sea level near the lower portion of the intertidal zone where air exposure time is relatively short. The distribution area and biomass of benthic macroalgae gradually decreased during the study period. The surface sediments in the benthic algal region were mainly composed of finer sediments, such as slightly gravelly mud and mud. The temperature, salinity, pH, and nutrient concentrations (except dissolved inorganic nitrogen) in pore water did not differ in regions with and without benthic macroalgae, whereas the mean grain size and the concentrations of IL, COD, and AVS in sediments were much higher in regions harboring benthic macroalgae. The correlation between mean grain size and IL in sediments displayed two distinct gradients and the slope was much steeper in regions harboring benthic macroalgae, indicating that the content of organic matter in benthic algal region is not solely dependent on mean grain size. Our results indicate that the benthic macroalgae in the southern intertidal zone of Hampyeong Bay play an important role in the accumulation of organic matter in sediment.