In rural settings of Côte d’Ivoire, access to water, sanitation, and hygiene (WASH) at schools is often lacking. The purpose of this study was to assess the availability, quality, and use of WASH infrastructure in schools in the south-central part of Côte d’Ivoire, and to determine the hygiene practices of schoolchildren. A cross-sectional study was conducted in 20 primary schools with (n = 10) or without (n = 10) direct access to drinking water. The survey was comprised of a questionnaire directed at schoolchildren aged 8–17 years, an assessment of the WASH infrastructure, and the testing of drinking water samples for Escherichia coli and total coliforms. Overall, 771 schoolchildren were enrolled in the study. One out of four children (24.9%) reported that they used available toilets. Among those children not using toilets, more than half (57.5%) reported that they practised open defecation. Drinking water infrastructure was limited in most schools because of poor storage tanks, the low flow of water, or broken wells. All drinking water samples (n = 18) tested positive for total coliforms and 15 (83.3%) tested positive for E. coli. The lack of WASH infrastructures in primary schools in the south-central part of Côte d’Ivoire, in combination with poor hygiene practices, might govern disease transmission and absenteeism at school, especially among females.