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This is list of major wetlands in Estonia. The list is incomplete.

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Avaste Nature Reserve is a nature reserve situated in western Estonia, to largest extent in Pärnu County.

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Järveküla Nature Reserve is a nature reserve founded in 1990, situated by Lake Vörtsjärv in southern Estonia near the village of Järveküla. The nature reserve has been established to protect the population of white-tailed eagles present in the area, and includes pine forest and patches of bog.

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Lindi Nature Reserve is a nature reserve situated in south-western Estonia, in Pärnu County.

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Luitemaa Nature Reserve is a nature reserve situated in south-western Estonia, in Pärnu County.

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Nätsi-Võlla Nature Reserve is a nature reserve situated in western Estonia, in Pärnu County, made up of several bogs that together form the largest bog area in Pärnu County.

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Parika Nature Reserve is a nature reserve in Viljandi County in southern Estonia.

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Pihla-Kaibaldi Nature Reserve is a nature reserve situated on Hiiumaa in western Estonia, in Hiiu County.

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Raudna Nature Reserve is a nature reserve situated in southern Estonia, in Viljandi County.

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Rubina Nature Reserve is a nature reserve in Viljandi County in southern Estonia.

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Silma Nature Reserve is a nature reserve situated in south-western Estonia, in Lääne County.

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Tihu Nature Reserve is a nature reserve situated on Hiiumaa in western Estonia, in Hiiu County.

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Tündre Nature Reserve is a nature reserve situated in southern Estonia, straddling the border between Viljandi and Valga County.