From April 1994 to April 1996, we carried out monthly surveys on the physical and chemical variability of ebbing water at two intertidal stations near the emerged tidal flat and surface water at a nearby subtidal station, in a tidal estuary of the Seto Inland Sea, Japan. The fresh water runoff was a major source of new nitrogen (nitrate + nitrite = −2.1 × salinity + 74.3, r2 = 0.76, p < 0.001, at the inner intertidal station). In contrast, the absence or weak correlation of ammonium, phosphate and silicate with salinity in ebbing water highlighted the importance of in situ biologically-mediated processes, including the excretory activity of intertidal dominant bivalves (Ruditapes philippinarum and Musculista senhousia) and primary producer nutrient uptake. Among suspended particulate matter (SPM), the negative correlation of Chl a with salinity (p< 0.001) suggested that an upper intertidal zone, where high microphytobenthic assemblages occur, may represent a considerable source of microalgal biomass. Whereas, a stronger correlation of POC with pheo-pigments (r2 ≥ 0.92) than with Chl a (r2 ≤ 0.44), a low fraction of living phyto-Carbon (ca. 5%) and a high pheo-pigment/Chl a ratio (ca. 3) indicated a high portion of refractory algal material and a close water–sediment coupling on the flat, in which abundant macrozoobenthos is likely to play an important role. In spite of the strong variability of this ecosystems, this study also demonstrated that highly significant seasonal patterns can be recognized in our study area. However, patterns varied depending on the different nutrient species, SPM and sites. In ebbing water, ammonium concentrations were significantly higher in the cold period (i.e. November–April: water temperature 10.0 ± 4.4 °C), when primary producer biomass decreases, while Chl a and pheo-pigment content were 4.3 and 4.8 higher in the warm period (May–October: water temperature 23.5 ± 4.2 °C), respectively. At the subtidal site, nutrients were 1.9 (silicate)–2.9 (phosphate) and SPM was 1.8 (POC)–2.1 (pheo-pigments) times higher in the warm period. On an annual basis, mean pheo-pigment and POC content was 12–25 times and 4–8 times higher on the intertidal zone than on the subtidal zone, respectively, while nutrient concentrations were within the same order of magnitude. Such a qualitative difference (i.e. nutrients vs. SPM) between sites suggests that particle deposition and/or removal is likely to occur along the estuary, resulting in a limited SPM content at the surface layer of the subtidal site, while nutrients are more directly transported into the surface layer of the subtidal zone by lower salinity water mass intrusion from the intertidal zone, most importantly during the warm period.
