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For the 2025-26 school year, there are 2 public middle schools serving 647 students in Watertown, SD.

The top ranked public middle schools in Watertown, SD are Watertown Middle School - 02 and Waverly-south Shore Middle School - 03. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Watertown, SD public middle schools have an average math proficiency score of 47% (versus the South Dakota public middle school average of 39%), and reading proficiency score of 62% (versus the 49% statewide average). Middle schools in Watertown have an average ranking of 9/10, which is in the top 20% of South Dakota public middle schools.

Minority enrollment is 17% of the student body (majority Hispanic), which is less than the South Dakota public middle school average of 42% (majority American Indian).