The water environment of Ariake Bay has been degraded for decades, with some observers suggesting that this problem might be due to the decrease in tidal flat areas. However, for lost tidal flats, the water purification capacity cannot be estimated without sufficient historical data. A new procedure for estimating the water purification capacity of the Isahaya Tidal Flat (i.e., a lost tidal flat) was developed based on an ecosystem model. Given their similarities, an ecosystem model was first developed for the tidal flats of the Shiota River, and then recalibrated using the limited historical data available for the Isahaya Tidal Flat. The water purification capacity of the Isahaya Tidal Flat was estimated to be 0.39 t-N d^-1 in 1988, when the tidal flat covered a total area of 35.64 km², which is equivalent to just 36% of total nitrogen loading from the basin (1.07 _t-N d^-1). The denitrification capacity of the Isahaya Tidal Flat was shown to be 7.3 × 10^-3 _t-N km^-2 d^-1. Both the water purification capacity and denitrification capacity estimated for the muddy Isahaya Tidal Flat were much less than those of sandy tidal flats (e.g., tidal flats at Sambanse).