The water crisis in Jackson, Mississippi, has recently made national and international headlines as a major environmental catastrophe, impacting the public health and wellbeing of residents.

Here we focus on Jackson’s most prevalent and vulnerable population, its children, by assessing how boil water alerts (BWAs) disrupt student learning. Using data on BWAs collected from the City of Jackson’s Water/Sewer Business Administration Office between 2015 and 2021, daily school attendance data from Jackson’s Public School District and community- level vulnerabilities from the American Community Survey, we add an important layer to the current conversation by analysing how BWAs disrupt student learning. After adjusting for community-level vulnerabilities, we show that each time a BWA is issued, unexcused absence rates statistically significantly increase by 1–10%. We also show statistically significant decreases in unexcused absences in schools where much of the student body receives free and reduced lunches. In a city that releases hundreds of BWAs each year, our findings highlight the urgency for addressing the root causes of the poor water quality in Jackson.