自91年起建立海域水質變化資料庫並統籌辦理全國海域環境水質監測工作，海域水質環境分為甲類、乙類及丙類，擇定主、次要河川入海口、重要污染源流入點、港灣、潟湖、一般海域水質背景點、自然保留區、生態保育區、國家公園生態保護區、特別景觀區、遊憩區、野生動物保護區及水產資源保育區等105處進行水質採樣監測，112年起加入強化海域代表點20處，並將監測結果定期公告（iOcean海洋保育網 )，91年至113年海域水質監測歷年達成率為97.9%以上。
| 年度 | 監測對象 | 海域水質達成率 | 總達成率 | ||||||
|---|---|---|---|---|---|---|---|---|---|
| pH | 溶氧 | 鎘 | 鉛 | 鋅 | 汞 | 銅 | |||
| 91 | 近海97處海域測站 | 94.1% | 95.4 | 100% | 100% | 100% | 98.7% | 97.4 | 97.9% |
| 92 | 98.5% | 99.7% | 100% | 100% | 100% | 99.7% | 100% | 99.7% | |
| 93 | 98.7% | 99.2% | 100% | 100% | 100% | 100% | 100% | 99.7% | |
| 94 | 近海104處海域測站 | 99.0% | 99.0% | 100% | 100% | 100% | 100% | 100% | 99.7% |
| 95 | 99.5% | 100% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 96 | 99.3% | 100% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 97 | 99.7% | 100% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 98 | 99.8% | 99.5% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 99 | 100% | 99.5% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 100 | 100% | 99.5% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 101 | 近海105處海域測站 | 99.3% | 97.9% | 100% | 100% | 100% | 100% | 100% | 99.6% |
| 102 | 99.8% | 99.8% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 103 | 99.5% | 99.8% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 104 | 100% | 99.0% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 105 | 99.5% | 99.3% | 100% | 100% | 100% | 100% | 100% | 99.8% | |
| 106 | 99.3% | 100% | 100% | 100% | 100% | 100% | 99.8% | 99.9% | |
| 107 | 99.0% | 99.5% | 100% | 100% | 100% | 100% | 99.3% | 99.7% | |
| 108 | 98.1% | 91.7% | 100% | 99.4% | 100% | 100% | 100% | 98.5% | |
| 109 | 99.8% | 100% | 100% | 100% | 100% | 100% | 99.5% | 99.9% | |
| 110 | 99.3% | 99.8% | 100% | 100% | 100% | 100% | 99.5% | 99.8% | |
| 111 | 99.3% | 100% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
| 112 | 近海125處海域測站 | 100% | 100% | 100% | 100% | 100% | 100% | 100% | 100% |
| 113 | 99.5% | 100% | 100% | 100% | 100% | 100% | 100% | 99.9% | |
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