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) supplied by natural weathering. The consequent decrease in the DSi supply to the sea is advantageous to flagellates (nonsiliceous and potentially harmful) but not to diatoms (siliceous and mostly benign) in coastal marine ecosystems. Verification of this hypothesis has been hampered by lack of relevant data, particularly in Asia. We investigated the aquatic continuum composed of Lake Biwa, the Yodo River, and the Seto Inland Sea, Japan, where the natural conditions make the silica deficiency less 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 relative dominance of diatom and flagellates could not be explained solely by the stoichiometric arguments but by the supportive discussion on the difference of their 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/N ratio 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 loaded directly. The rate of DSi retention correlated with socio-economic changes, such as rapid economic growth in the 1960s and mitigations implemented after the 1980s. Sensitivity of this continuum to the Si processes suggests the global significance of this hypothesis.