| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| Aileen Colburn Elementary School | K-6 | 2201 Heller Street
Atwater, CA | 95301 | (209) 357-6136 | Merced | public | Atwater Elementary |
| Atwater High School | 9-12 | 2201 Fruitland Avenue
Atwater, CA | 95301 | (209) 357-6000 | Merced | public | Merced Union High |
| Atwater Junior Academy | n/a | 1434 California Street
Atwater, CA | 95301 | (209) 357-6100 | Merced | public | Atwater Elementary |
| Atwater Senior Academy | 7-8 | 1800 Juniper Avenue
Atwater, CA | 95301 | (209) 357-6515 | Merced | public | Atwater Elementary |
| Bellevue Elementary School | K-8 | 1020 East Bellevue Road
Atwater, CA | 95301 | (209) 357-6140 | Merced | public | Atwater Elementary |
| Buhach Colony High School | 9-12 | 1800 Buhach Road
Atwater, CA | 95301 | (209) 357-6600 | Merced | public | Merced Union High |
| Central Valley Christian School | K-12 | 2457 Man O War Court
Atwater, CA | 95301 | (209) 722-7799 | Merced | private | |
| Elmer Wood Elementary School | K-6 | 1271 West Bellevue Road
Atwater, CA | 95301 | (209) 357-6143 | Merced | public | Atwater Elementary |
| King's Christian Academy | 2, 4-6 | 1683 5th St
Atwater, CA | 95301 | (209) 357-5691 | Merced | private | |
| King's Christian School | K-8 | 1683 Fifth Street
Atwater, CA | 95301 | (209) 357-5691 | Merced | private | |
| Landmark Christian School | K-12 | 1925 Olive Avenue
Atwater, CA | 95301 | (209) 358-0790 | Merced | private | |
| Mitchell Elementary School | K-6 | 1761 Grove Avenue
Atwater, CA | 95301 | (209) 357-6112 | Merced | public | Atwater Elementary |
| Mitchell Intermediate School | 7-8 | 1753 Fifth Street
Atwater, CA | 95301 | (209) 357-6124 | Merced | public | Atwater Elementary |
| Peggy Heller Elementary School | K-6 | 201 Lake View Drive
Atwater, CA | 95301 | (209) 357-6517 | Merced | public | Atwater Elementary |
| Shaffer Elementary School | K-6 | 1434 California Street
Atwater, CA | 95301 | (209) 357-6145 | Merced | public | Atwater Elementary |
| St. Anthony School | PK-8 | 1801 Winton Way
Atwater, CA | 95301 | (209) 358-3341 | Merced | private | |
| Thomas Olaeta Elementary School | K-6 | 2266 High Street
Atwater, CA | 95301 | (209) 357-6148 | Merced | public | Atwater Elementary |
| Valley Atwater Community Day School | 7-12 | 1800 Matthew Avenue
Atwater, CA | 95301 | (209) 381-4550 | Merced | public | Merced County Office of Education |
