Consistent and effective practice of water treatment, sanitation, and hygiene (WASH) behaviour is an indispensable requisite for realizing health improvements among children living in low-income areas with challenging hygienic conditions. Sustainably achieving such a behaviour change is challenging but more likely to be realized during epidemics, when health threats are high and the dissemination of information on preventative measures is intense. Our study conducted cross-sectional surveys in Surkhet District Nepal, before and during the Covid-19 pandemic to assess the impact of water safety interventions and hygiene training implemented before and during the pandemic on WASH conditions and practices and to assess the association of these changes with child health. Information on WASH infrastructure, WASH behaviour, nutrition, and child health, including on parasitic infections, was obtained before and during the Covid-19 pandemic in spring 2018 and spring 2021, from 589 children aged between 6 months and 10 years and their caregivers. Data was collected through quantitative, structured face-to-face interviews, observations, health examinations of children including anthropometric measurements, analysis of children's stool, and water quality analysis. The association of changes in WASH factors with changes in child health was analysed using multivariate generalized estimating equations for repeated measures. Water safety management was significantly improved by the introduction of chlorination to piped water supply systems, which served 40% of households. In addition, the percentage of households using a ceramic water filter increased from 12.2% to 34.8%. Large and significant changes were observed in handwashing behaviour (frequency, use of soap and washing at critical times) and infrastructure: 35% of households constructed a new handwashing station. Kitchen and household hygiene also improved. An additional 22% of households improved the cleanliness of the toilet. The number of houses with a cemented floor increased by 20%. WASH changes were significantly associated with improved child health: the chlorination of piped water supply reduced odds ratios for diarrhoea (OR=0.36, 95% CI=0.15-0.88, p=0.025), respiratory difficulties (OR=0.39, 95% CI=0.16-0.92, p=0.033), fever (OR=0.42, 95% CI=0.26-0.71, p=0.001) and cough (OR=0.58, 95% CI=0.36-0.93, p=0.024), and. The frequency of handwashing with soap was associated with significantly reduced odds ratios for infections with Giardia lamblia (OR=0.68, 95% CI=0.50-0.91, p=0.011), stunting and wasting (OR=0.75, 95% CI=0.66-0.92, p=0.003) and fever (OR=0.85, 95% CI=0.75-0.96, p=0.008),. The presence of a handwashing station at baseline was associated with significantly reduced odds ratios for respiratory difficulties (OR=0.45, 95% CI=0.26-0.78, p=0.004). The construction of a handwashing station between baseline and endline was significantly associated with reduced odds ratios for pale conjunctiva (OR=0.32, 95% CI=0.17-0.60, p<0.001), which is a clinical sign of iron deficiency and anaemia, respiratory difficulties (OR=0.39, 95% CI=0.17-0.89, p=0.026) and cough (OR=0.44, 95% CI=0.26-0.76, p=0.003). Using a clean container for the transport of drinking water was significantly associated with reduced odds ratios for infections with Giardia lamblia (OR=0.39, 95% CI=0.16-0.93, p=0.033) and diarrhoea (OR=0.48, 95% CI=0.24-0.96, p=0.038). Similarly, a cemented floor in the household was significantly associated with reduced odd ratios for diarrhoea (OR=0.38, 95% CI=0.16-0.87, p=0.022) and infections with Giardia lamblia (OR=0.44, 95% CI=0.19-1.02, p=0.056). WASH training and the promotion of preventative measures during the Covid-19 pandemic supported improved water safety management and hygiene behaviour, which resulted in a reduction in infectious diseases among children in the study area.