Abstract Background Despite a strong theoretical rationale for combining water, sanitation and hygiene (WaSH) interventions to improve child health, study findings are heterogeneous with little understanding of the mechanisms for these effects. Our study objective was to demonstrate the utility of structural equation modeling (SEM) to assess intervention effects on height-for-age z score (HAZ) through the complex system of WaSH pathways. Methods We used data from a matched cohort effectiveness evaluation of a combined on-premise piped water and improved sanitation intervention in rural Odisha, India. Height/length was measured in children 0–59 months old (n = 1826) from 90 matched villages in February–June 2016. WaSH behaviours and infrastructure were assessed through household surveys and observation, respectively. We used SEM to calculate the standardized path coefficients and the total contributions of WaSH pathways to HAZ. Results Intervention improvements on HAZ were through the sanitation pathway (coverage → use β: 0.722; use → HAZ β: 0.116), with piped water coverage indirectly affecting HAZ through improved sanitation use (β: 0.148). Although the intervention had a positive association with handwashing station coverage, there was no evidence of a total hygiene pathway effect on HAZ or further direct effects through the water pathways. Conclusions This study demonstrates the utility of SEM to assess the mechanisms through which combined WaSH interventions impact HAZ as a system of pathways, providing a more nuanced assessment than estimation of the total intervention effect. Our finding, that water impacts HAZ through the sanitation pathway, is an important and actionable insight for WaSH programming.