A mass balance of dissolved silica (DSi) based on daily measurements at the inflow and outflow of the Three Gorges Reservoir (TGR) in 2007 and a more precise budget, with inflow, outflow, primary production, biogenic silica (BSi) settlement, dissolution of BSi in the water column and flux of DSi at the sediment–water interface in the dry season (April) of 2007 were developed. We address the following question: How much does the Three Gorges Dam (TGD) affect silica transport in the TGR of the Changjiang River (Yangtze River)? The DSi varied from 71.1 to 141 μmol/l with an average of 108 μmol/l, and it ranged between 68.1 and 136 μmol/l, with an average of 107 μmol/l in inflow and outflow, respectively, in the TGR in 2007. The linear relationship of DSi between inflow and outflow water is significant (r = 0.87, n = 362, p < 0.01). Along the main stream of the TGR, the DSi concentration decreases with an average concentration of 84.0 μmol/l in the dry season. However, the stratification of DSi was not obvious in the main channel of the TGR in the dry season. The BSi is within the range of 0.04–5.00 μmol/l, with an average concentration of 2.1 μmol/l in the main channel of the TGR, while it is much higher in Xiangxi Bay (1.30–47.7 μmol/l, 13.1 μmol/l) than in the main stream of the TGR and the other bays. After the third filling of the TGR, approximately 3.8% of the DSi was retained by the TGR based on a 12-month monitoring scheme in 2007, which would slightly reduce nutrient fluxes of the Changjiang River to the East China Sea (2%). DSi was lost during January to June and November, whereas the additions of DSi were found during the other months in 2007. The budget results also indicate that there is a slight retention of DSi. The retention of DSi in the reservoir is approximately 2.9%, while BSi is approximately 44%. Compared with the total silica load, the retention of DSi and BSi in the reservoir is only 5.0% in the dry season. With its present storage capacity, the reservoir does not play an important role as a silica sink in the channel of the TGR. The DSi load is significantly related to discharge both in inflow and outflow waters (p < 0.01). DSi retention, to some extent, is the runoff change due to impoundment.
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