本研究應用世界自然基金會的保護區經營管理快速評估與設定優先法（WWF RAPPAM Methodology），綜整個別與系統方法取徑，配合參與式工作坊、文獻回顧、參與觀察與訪談，評估臺灣現有除國家公園外的11座海岸河口溼地型保護區，總計13個個案的經營管理效能，以及所面臨的壓力與威脅，探究臺灣整體海岸河口溼地型保護區面臨的問題與挑戰。評估結果顯示，海岸河口溼地型保護區普遍面臨漁撈與收穫水殖產品、遊憩活動、入侵種、家庭污水和都市廢水、垃圾和固體廢物衝擊等問題。其中，污染最為普遍。由於大部分的威脅來自於保護區外，管理單位難以因應。13個個案中的7個，其經營管理效能有類似的趨勢：經營管理目標清楚、溝通與資訊良好、基礎設施表現佳，但位置的設計與規劃不佳、人力資源與財務不足、經營管理計畫不完全及監測、研究與評估較弱，其他持平。系統評估顯示臺灣海岸河口溼地型保護區系統的設計、政策及其政策環境皆不佳。將海岸河口溼地型保護區以保育目標與棲地完整性分成4類，不考慮保育目標差異較大的紅樹林保護區，範圍大具完整生態系者的保育優先性，高於範圍小多人為干擾與半人工溼地。整體而言，曾文溪口北岸黑面琵鷺保護區、高美野生動物保護區為最需要列為保育優先者。另，本研究的經驗發現，要做好系統評估需要足夠的基礎資料與清楚的範疇，宜先依保育目標分類並確保多元的參與者。

This study applies the Rapid Assessment and Prioritization of Protected Area Management (RAPPAM) methodology of the WWF, to evaluate the pressures and threats, management effectiveness of eleven coastal and estuarine protected areas (thirteen cases) in Taiwan, and to analyze their influential factors. This study implements respectively evaluation at both site-level and the system-level, through participatory workshops, literature review, participant observation and interviews. The results showed that the coastal and estuarine protected areas generally encountered pressures and threats of fishing and harvesting aquatic resources, recreational activities, invasive non-native/alien species, household sewage and urban waste water, garbage and solid waste. While pollution was one of the most popular pressures and threats among them, this study revealed that most of them came from outside of protected areas which were difficult to handle by the management authorities. Seven of thirteen cases that have implemented site-level evaluation have a similar pattern on their management: clear objectives, good communications and information delivery, sufficient infrastructure, improper site design and planning, lacking human resources and financial supports, incomplete management planning and weak monitoring, research and evaluation. The results of system-level evaluation revealed that our coastal and estuarine protected areas faced poor policy environment, inappropriate protected area system-level design, and inadequate protected area policies. Based on conservation objective and habitat integrity, it can be divided into three categories for the coastal and estuarine protected areas. Excluding both mangrove protected areas, those of large coverage and intact ecosystem have higher priority on conservation than those of smaller ranges and more artificial interferences and semi-artificial wetlands. This study identified both Zengwun Rivermouth Black-faced Spoonbill Refuge and Gaomei Wetlands Wildlife Refuge should be listed on the top for conservation considerations. The results show that it needs sufficient baseline information, clear definition of range, classification first by conservation objectives and diversifiedreviewers in order to engage well the system evaluation work.