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We conducted a cluster-randomized water, sanitation, and hygiene trial in 185 schools in Nyanza province, Kenya. The trial, however, had imperfect school-level adherence at many schools. The primary goal of this study was to estimate the causal effects of school-level adherence to interventions on pupil diarrhea and soil-transmitted helminth infection.Schools were divided into water availability groups, which were then randomized separately into either water, sanitation, and hygiene intervention arms or a control arm. School-level adherence to the intervention was defined by the number of intervention components—water, latrines, soap—that had been adequately implemented. The outcomes of interest were pupil diarrhea and soil-transmitted helminth infection. We used a weighted generalized structural nested model to calculate prevalence ratio.In the water-scarce group, there was evidence of a reduced prevalence of diarrhea among pupils attending schools that adhered to two or to three intervention components (prevalence ratio = 0.28, 95% confidence interval: 0.10, 0.75), compared with what the prevalence would have been had the same schools instead adhered to zero components or one. In the water-available group, there was no evidence of reduced diarrhea with better adherence. For the soil-transmitted helminth infection and intensity outcomes, we often observed point estimates in the preventive direction with increasing intervention adherence, but primarily among girls, and the confidence intervals were often very wide.Our instrumental variable point estimates sometimes suggested protective effects with increased water, sanitation, and hygiene intervention adherence, although many of the estimates were imprecise.