This is list of bays in Estonia. The list is incomplete.
| Name | Location | Further info | Image | Coordinates |
|---|---|---|---|---|
| Ariste Bay | ||||
| Atla Bay | ||||
| Eeslaht (Haapsalu Eeslaht) | Part of Haapsalu Bay | |||
| Eru Bay | Part of Gulf of Finland | 59°36′N 25°49′E / 59.600°N 25.817°E | ||
| Gulf of Riga | Part of Baltic Sea | |||
| Haapsalu Bay | ||||
| Hara Bay | 
|
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| Hellamaa Bay | ||||
| Jausa Bay | ||||
| Kakumäe Bay | Part of Tallinn Bay | |||
| Kasselaht | ||||
| Kasti Bay | ||||
| Kopli Bay | Part of Tallinn Bay | |||
| Tallinn Bay | Part of Gulf of Finland | 
|
59°31′8″N 24°40′6″E / 59.51889°N 24.66833°E | |
| Roadstead of Tallinn | Part of Tallinn Bay | |||
| Harju Bay | Saare County | Nowadays a lake. | ||
| Kaugatoma Bay | ||||
| Kolga Bay | ||||
| Käsmu Bay | ||||
| Kahvatu Bay | Nowadays a lake. Its area is 5.2 ha. | |||
| Lahepere Bay | ||||
| Linnulaht | Nowadays a lake. | |||
| Lohusalu Bay | Harju County | |||
| Matsalu Bay | Lääne County | |||
| Narva Bay | Part of Gulf of Finland | 
|
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| Oessaare Bay | Saare County | Now a lake, formerly a bay | ||
| Õunaku Bay | Hiiu County | Same as Salinõmme Bay | ||
| Paljassaare Bay | Part of Tallinn Bay | |||
| Pärnu Bay | Part of Gulf of Riga | Its area is 411 km². | 
|
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| Saastna Bay | Width of 3.8 km | |||
| Soonlepa Bay | Hiiu County | |||
| Suur Katel | Its area is 158 km². | |||
| Suuremõisa Bay | ||||
| Tagalaht | 
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| Vaemla Bay | Hiiu County |