Background: Providing universal access to safe water, sanitation and hygiene (WASH) in remote Nepal remains challenging. We investigated WASH conditions and their association with children's nutritional status, intestinal parasitic infections and diarrhoea. Methods: Data was collected through a cross-sectional survey of 1427 households, including questionnaires, observations, stool analysis, anthropometry, water quality measurements, and assessment of clinical signs of nutritional deficiencies. Results: We found 55.5% of children were undernourished, 63.9% had clinical signs of nutritional deficiencies, 51.1% had intestinal parasitic infections and 52.2% had diarrhoea. Multivariate mixed logistic regression analysis revealed a statistically significant negative association between undernutrition and socioeconomic level, with adjusted odds ratios (AOR) of 0.70 (95%-CI = 0.43-1.11) and 0.43 (95%-CI = 0.25-0.75) for high and intermediate levels compared to the lowest level. Undernutrition was negatively associated with regular deworming of children (AOR = 0.44, 95% CI = 0.20-0.94), food supplements (AOR = 0.57, 95% CI = 0.38-0.84), household's own food production (AOR = 0.67, 95% CI = 0.46-0.97) and personal hygiene (AOR = 0.83, 95% CI = 0.51-1.35). Nutritional deficiency was negatively associated with handwashing after cleaning a baby's bottom (AOR = 0.60, 95% CI = 0.40-0.92) and cleanliness of caregiver's hands (AOR = 0.61, 95% CI = 0.41-0.89) and positively associated with keeping animals inside the house overnight (AOR = 1.71, 95% CI = 1.17-2.51) and the presence of total coliforms in the drinking water source (AOR = 10.44, 95% CI = 1.61-67.4). Diarrhoea was positively associated with intermittent water supply (AOR = 2.72, 95% CI = 1.18-6.31) and the presence of a mud floor (AOR = 2.29, 95% CI = 1.20-4.37) and negatively associated with cleanliness of the toilet (AOR = 0.68, 95% CI = 0.47-0.98), and the cleanliness of children's hands (AOR = 0.62, 95% CI = 0.40-0.96).