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For the 2026 school year, there are 10 public schools serving 3,788 students in Watertown, SD (there are , serving 585 private students). 87% of all K-12 students in Watertown, SD are educated in public schools (compared to the SD state average of 91%).

The top-ranked public schools in Watertown, SD are Lincoln Elementary - 05, Mckinley Elementary - 06 and Watertown Middle School - 02. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Watertown, SD public schools have an average math proficiency score of 48% (versus the South Dakota public school average of 43%), and reading proficiency score of 59% (versus the 51% statewide average). Schools in Watertown have an average ranking of 8/10, which is in the top 30% of South Dakota public schools.

Minority enrollment is 17% of the student body (majority Hispanic), which is less than the South Dakota public school average of 33% (majority American Indian).