BackgroundOverweight among adolescents remains a serious concern worldwide and can have major health consequences in later life, such as cardiovascular diseases and cancer. Still, 33% of secondary school adolescents in the Netherlands consume sugar-sweetened beverages daily and over 26% do not consume water every day. The Dutch Healthy School program was developed to support schools in stimulating healthier lifestyles by focusing on health education, school environments, identifying students’ health problems, and school policy. We examined the variation between secondary schools regarding the daily consumption of water and sugar-sweetened beverages and whether this variation can be explained by differences between schools regarding Healthy School certification, general school characteristics, and the school population.MethodsWe performed a cross-sectional multilevel study. We used data from the national Youth Health Monitor of 2019 on secondary schools (grades 8 and 10, age range about 12 to 18 years) of seven Public Health Services and combined these with information regarding Healthy School certification and general school- and school population characteristics. Our outcomes were daily consumption of water and sugar-sweetened beverages. In total, data from 51,901 adolescents from 191 schools were analysed. We calculated the intraclass correlation to examine the variation between schools regarding our outcomes. Thereafter, we examined whether we could explain this variation by the included characteristics.ResultsThe school-level explained 4.53% of the variation in the consumption of water and 2.33% of the variation in the consumption of sugar-sweetened beverages. This small variation in water and sugar-sweetened consumption could not be explained by Healthy School certification, yet some general school- and school population characteristics did: the proportion of the school population with at least one parent with high educational attainment, the educational track of the adolescents, urbanicity (only for water consumption) and school type (only for sugar-sweetened beverages consumption).ConclusionsThe low percentages of explained variation indicate that school-level characteristics in general (including Healthy School certification) do not matter substantially for the daily consumption of water and sugar-sweetened beverages. Future research should examine whether school health promotion can contribute to healthier lifestyles, and if so, under which level of implementation and school conditions.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16123-7.