阿公店水庫為全台唯一一個定期實施空庫排淤操作之水庫，然而在空庫排淤操作時期，會使水庫某些水質呈現惡化情況，造成水庫被評估為優養。阿公店水庫方於2006年完成更新、操作不到10年常被視為優養，空庫排淤確為原因之ㄧ。有鑒於空庫排淤所造成水質之惡化問題，針對空庫排淤時期之水質管理變得相當重要，但因利用一般二維水理水質模式並無法有效模擬出空庫排淤時期之變化；因此本研究係將阿公店水庫分成蓄水時期與空庫排淤時期，並將各時期於2008年至2013年各分為五段，再利用CE-QUAL-W2水理水質模式，以變網格方式分別建立各期間之適當網格進行水庫水理及水質模擬，同時探討不同時期水庫之涵容能力。
分析結果顯示，以CE-QUAL-W2模擬阿公店水庫水位、水溫等水理現象，模擬結果為可被接受。本研究另針對優養化相關因子進行水質分析，分別探討懸浮固體物、葉綠素a、總磷、總氮、溶氧及總有機碳。懸浮固體物、總磷及總氮模擬結果在降雨發生後都會有波峰產生，但其他天數則會有低估情形；相對地，葉綠素a整體而言則會有高估情形。但是一維網格在降雨發生後都會造成葉綠素a降低；而總有機碳模擬情形之趨勢大致上與葉綠素a相似。
分析阿公店水庫不同時期之涵容能力發現，一維網格平均涵容能力都較二維網格時期低，而一維網格時期於透明度分析上並無涵容能力；若針對空庫排淤時期改善水庫水質，會使得污染改善成本太高，且改善效率不如預期。綜合上述結果得知，若針對阿公店水庫進行全年度優養化指標分析時，若無重大用水考量，則建議不要將空庫排淤時期列入考量；針對蓄水時期之污染改善策略建議可針對越域引水水質以及集水區內農業灌溉進行改善，將可有效改善蓄水時期水庫優養化之現象。

Agongdian Reservoir is the only reservoir in Taiwan that regularly uses an empty flushing strategy for desiltation. The empty flushing method involves the use of reservoir inflow to wash away sediment from the reservoir bottom by transferring the sediment further downstream. Main sources of Agongdian Reservoir water inflow include: cross-watershed diversion, rainfall runoff, direct channel precipitation, and water coming from the ZuoShui and WangLai Rivers within the reservoir’s catchment. The objective of this study is to build up a suitable water quality model for an empty flushing reservoir. The methodology for this study was therefore split into three stages. First, the modeling strategies in the Agongdian Reservoir were divided into two periods alternating between the storage period and the empty flushing period. Second, a variable grid was established for each period of water quality modeling. Third, the assimilative capacity of the reservoir to receive pollutants at different periods were then compared and analyzed. The results of this study show: (1) Using acceptable water levels (i.e. RMSE< 0.539) and water temperatures (i.e. AME < 1.678) is a good indicator that simulated water quality results in this study are robust. (2) Based on the water quality model, rainfall is the major source of inflow pollution during periods of empty flushing. In addition, during the water storage period, cross-watershed diversion is another important factor to consider. (3) The empty flushing period has a relatively lower carrying capacity compared to the water storage period, where sediment has time to settle on the bottom. The lower carrying capacity is due to multiple factors including: sediment remaining suspended in the water column, re-suspension of sediment settled on the reservoir bottom, which thereby causes release of phosphate and nitrogen into the water body. Based on these findings in the Agongdian Reservoir, this study suggests that because of lower carrying capacity, improvement of water quality during empty flushing period is an unnecessary additional cost. So, unlike other reservoirs in Taiwan, eutrophication analysis for the Agongdian Reservoir should be considered only during the water storage period.

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