Abstract Introduction Inadequate nutrition in early life and exposure to sanitation-related enteric pathogens have been linked to poor growth outcomes in children. Despite rapid development in Cambodia, high prevalence of growth faltering and stunting continue to persist. This study aimed to assess nutrition and WASH variables and their association with nutritional status of children under 24 months in rural Cambodia. Methods We conducted surveys in 491 villages across 55 rural communes in Cambodia in September 2016 to measure associations between child, household, and community-level risk factors for stunting and length-for-age z-score (LAZ). A primary survey measured child-level variables, including anthropometric measures and risk factors for growth faltering and stunting, for 4,036 children under 24 months of age from 3,877 households (approximately 8 households per village). For LAZ, we calculated bivariate and adjusted associations (as mean differences) with 95% confidence intervals using generalised estimating equations (GEEs) to fit linear regression models with robust standard errors. For stunting, we calculated unadjusted and adjusted prevalence ratios (PRs) with 95% confidence intervals using GEEs to fit Poisson regression models with robust standard errors. For all models assessing effects of household-level variables, we used GEEs to account for clustering at the village level. Results After adjustment for potential confounding, presence of water and soap at a household’s handwashing station was found to be significantly associated (p<0.05) with increased LAZ (adjusted mean difference in LAZ +0.10, 95% CI: 0.03, 0.16), and household use of an improved drinking water source was associated with less stunting in children compared to households that did not use an improved source of drinking water (aPR 0.81, 95% CI: 0.66, 0.98); breastfeeding was associated with a lower LAZ score (−0.16, 95% CI: −0.27, −0.05). No other feeding practices (i.e., dietary diversity, meal frequency, minimum acceptable diet) or sanitation variables (i.e., household’s safe disposal of child stools, household-level sanitation, community-level sanitation) were associated with LAZ scores or stunting in children under 24 months of age. In an age-stratified analysis, children under 12 months of age were longer (LAZ +0.12, 95% CI: 0.02, 0.21) if there was presence of water and soap at the household handwashing station; at the community level, higher prevalence of shared sanitation (percentage of households in a village who report to use shared sanitation facilities) was negatively associated with child length (LAZ - 0.36, 95% CI: −0.66, −0.07).