Legionella contamination in public water systems poses significant health risks, particularly in schools where vulnerable populations, including children, regularly use these facilities. This study investigates the presence of Legionella in the hot water systems from 49 primary schools across two municipalities in the Danish capital region. Water samples were collected from taps in each school, and both first-flush and stabile temperature samples were analysed for Legionella contents. The findings revealed that 97% of schools in Municipality 1 and 100% in Municipality 2 had Legionella in their hot water systems. The content of Legionella colonies was significantly higher in schools in Municipality 1, which was probably because of overall lower water temperatures. At stabile temperatures, 76% and 50% of the schools in the two municipalities exceeded the European Union's recommended limit of 1000 CFU/L. Stabile peripheral water temperatures were achieved after 3 min. Tap water temperatures above 54 °C and central tank temperatures above 59 °C were associated with Legionella contents below 1000 CFU/L. This study highlights the need for more stringent Legionella control procedures in schools, including higher water temperatures and refining Legionella reducing interventions with the addition of regular flow and draining procedures.