The effect of rainfall on spatio-temporal variability of water quality and flow dynamics in the Shakujii and Sumida river estuaries was studied. The water level, salinity, turbidity, and flow velocity were observed for 12.5 hours after the occurrence of heavy rain on Nov. 11, 2016. Suspended sediment concentration (SSC) was analyzed. The results of the study showed mesotidal river estuaries having stratified to partially well mixed water columns. Rainfall brought a large freshwater discharge which caused the estuaries to be stratified, diminishing mixing and circulation in some stations. The saline water influx from Tokyo Bay was evident in the bottom layer of Sumida and Shakujii rivers while the buoyant freshwater flows in the upper layer. Comparing the different stations, Shakujii and upstream Sumida were largely affected by freshwater while downstream Sumida has a brackish water nature. Through the analysis of salinity and SSC, the phenomena of bottom sediment uplift, flocculation and erosion from local turbulent eddies were observed. Particulate organic matter and SSC relationship was also studied, which showed linear trend in the upstream while inorganic matter dominated the downstream. Other than rainfall, topography was identified to cause stratification. In Sumida river, deeper bottom depth decreased vertical mixing while in Shakujii river, salinity was retained due to bathymetry irregularities.

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