The silica deficiency hypothesis holds that increases of still waters caused byhydraulic alterations and high nitrogen (N) and phosphorus (P) discharges enhancethe growth of freshwater diatoms,which take up the dissolved silicate (DSi) suppliedby natural weathering.The consequent decrease in the DSi supply to the sea isadvantageous to flagellates (nonsiliceous and potentially harmful) but not to diatoms(siliceous and mostly benign) in coastal marine ecosystems.Verification of thishypothesis has been hampered by lack of relevant data,particularly in Asia.Weinvestigated the aquatic continuum composed of Lake Biwa,the Yodo River,andthe Seto Inland Sea,Japan,where the natural conditions make the silica deficiencyless likely to emerge due to the inherently rich supply of DSi.The results showedthat the silica was retained both in the lake and nearby the estuary.The relativedominance of diatom and flagellates could not be explained solely by thestoichiometric arguments but by the supportive discussion on the difference oftheir behavioral characteristics and the process nearby the estuary,where directinputs of N and P and effluent Si enhanced diatom bloom,even though the Si/Nratio was lowered in the upstream reservoir.Thus the retention of DSi occurred intwo places:in the lake and nearby the estuary,where the other N and P are loadeddirectly.The rate of DSi retention correlated with socio-economic changes,such asrapid economic growth in the 1960s and mitigations implemented after the 1980s.Sensitivity of this continuum to the Si processes suggests the global significance ofthis hypothesis. The silica deficiency hypothesis holds that increases of still waters caused by hydraulic alterations and high nitrogen (N) and phosphorus (P) discharges enhance the growth of freshwater diatoms, which take up the dissolved silicate (DSi) suppliedby natural weathering.The consequent decrease in the DSi supply to the sea isadvantageous to flagellates (nonsiliceous and potentially harmful) but not to diatoms (siliceous and mostly benign) in marine marine ecosystems.Verification of this hyphahesis has been hampered by lack of relevant data, particularly in Asia. We werevestigated the aquatic continuum composed of Lake Biwa, the Yodo River, and the Seto Inland Sea, Japan, where the natural conditions make the silica deficiencyless likely to emerge due to the inherently rich supply of DSi. The results showed that the silica was retained both in the lake and nearby the estuary. The relativedominance of diatom and flagellates could not be explained solely by thestoichiometric arguments but by the supportive d iscussion on the difference of the behavioral characteristics and the process nearby the estuary, where direct inputs of N and P and effluent Si enhanced diatom bloom, even though the Si / Nratio was lowered in the upstream reservoir.Thus the retention of DSi occurred in two places: in the lake and nearby the estuary, where the other N and P are loadeddirectly. The rate of DSi retention correlated with socio-economic changes, such as economic growth in the 1960s and mitigations after the 1980s. Sensitivity of this continuum to the Si processes suggests the global significance ofthis hypothesis