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For the 2025-26 school year, there are 4 public schools serving 3,005 students in Crystal River, FL (there are , serving 49 private students). 98% of all K-12 students in Crystal River, FL are educated in public schools (compared to the FL state average of 86%).

The top ranked public schools in Crystal River, FL are Academy Of Environmental Science, Crystal River Primary School and Crystal River Middle School. Overall testing rank is based on a school's combined math and reading proficiency test score ranking.

Crystal River, FL public schools have an average math proficiency score of 42% (versus the Florida public school average of 52%), and reading proficiency score of 45% (versus the 52% statewide average). Schools in Crystal River have an average ranking of 3/10, which is in the bottom 50% of Florida public schools.

Minority enrollment is 21% of the student body (majority Hispanic), which is less than the Florida public school average of 66% (majority Hispanic).