| Name | Address | Enrollment | Grade span |
|---|---|---|---|
| Eclipse Alternative School | 612 3RD ST NE | - | 7-10 |
| Garfield Elementary School | 216 10TH ST SE | - | 1-6 |
| Garfield Elementary School | 216 10TH ST SE | - | PK-K |
| Jefferson Elementary School | 1701 N MAPLE | - | PK-6 |
| Lake Area Multi-District School | 1311 THIRD AVENUE NE | - | 9-12 |
| Lincoln Elementary School | 1100 13TH ST NE | - | K-6 |
| Mckinley Elementary School | 5 12TH ST SW | - | K-6 |
| Mellette Elementary School | 619 2ND ST. NW | 322 | K-6 |
| Roosevelt Elementary School | 412 2ND ST SE | 297 | K-6 |
| Watertown High School | 200 NE 9TH ST | 1,251 | 9-12 |
| Watertown Junior High School | 601 11TH ST NE | 628 | 7-8 |
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