Background Severe acute malnutrition (SAM) affects approximately 12 million children globally. The aim of this study was to assess the effectiveness of integrating a household water treatment and hygiene promotion intervention within the national protocol of Senegal for outpatient treatment of children aged 6-59 months of age with uncomplicated SAM. Methods This was a pragmatic cluster-randomised controlled trial with health centres allocated 1:1 to receive either the standard protocol alone or the standard protocol with the addition of the water treatment and hygiene intervention. The primary outcome of the trial was SAM recovery defined under the national protocol in Senegal, and the secondary outcomes were weight gain, referral to inpatient care, enteric pathogen detection, diarrhoea, and all-cause mortality. Participants were followed up over eight weeks. Findings Between 22 December 2021 and 20 February 2023, 2411 children were enrolled in the study with 777 defaulting outpatient treatment during eight weeks of follow-up. There was no difference between control and intervention groups in the proportion of children recovering from SAM eight weeks post admission (39.8% vs 41.2%; adjusted odds ratio [aOR]: 0.97, 95% Confidence Interval [CI]: 0.66, 1.48). There was no difference in weight gain, referral, enteric pathogen detection or mortality between groups. The prevalence of diarrhoea at eight weeks follow-up was higher in the control group (20.0%) than the intervention group (12.5%), with evidence for a large difference between arms, accounting for between-group differences at baseline (aOR: 0.36; 95%CI: 0.26, 0.50). Interpretation The integration of household water treatment and hygiene promotion in the standard national protocol did not improve SAM recovery nor the related outcomes of weight gain, referral, enteric pathogen detection or mortality but did reduce diarrhoea. Our results suggest that the integration of this intervention to the standard protocol would not improve SAM outcomes in this setting but would potentially reduce the burden of diarrhoea among this vulnerable group. Funding This study was supported by the Bureau of Humanitarian Assistance of the United States Agency for International Development and the ACF Foundation.