To examine how tidal flat ecosystems develop and how they purify water, we deployed a tidal flat mesocosm system (TFMS). This system was composed of two types of sea sands with different grain size compositions, that is, fine and coarse sands (0.19 mm and 0.95 mm in median grain diameter, respectively) spread over experimental pools equipped with a tide generator. Seawater from Mikawa Bay was then introduced to the system. For about one year, fluctuations in the water quality of the reservoir and changes in sediment matters and benthic animals were monitored. Chlorophyll a concentration (Chl-a) in the water column was suppressed by macrobenthos, suggesting that the intake of Chl-a would be in proportion to the biomass of macrobenthos. Nitrogen content of detritus increased with the appearance of suspension-surface deposit feeders followed by meiobenthos and surface deposit feeders, which utilize the increased detritus. These observations were different from previous understanding that chemical changes in sediment matters control benthic communities. The biomass of macrobenthos and meiobenthos were larger in the tidal flat with coarse-grained sands than with fine-grained sands. DIN (dissolved inorganic nitrogen), DON (dissolved organic nitrogen) and PON (particulate organic nitrogen) in the water columns were removed and the estimated TN (total nitrogen) budget indicated that the removal rate (13%) in the coarse sand pool was larger than that (9%) in the fine sand pool. From these findings, it is clear that the purification function in the TFMS was established within one year.