Indonesia still faces several challenges in the areas of water, sanitation, and hygiene (WASH). Diarrhea remains a major killer of children and it is important to understand the local diarrhea transmission pathways to prioritise appropriate WASH interventions to reduce diarrhea burden. This study used a cross-sectional data set from a recent national household survey (the 2012 Indonesia Demographic and Health Survey) to examine the associations between diarrhea in children aged less than 24 months with WASH interventions and population characteristics. Unsafe disposal of child feces was strongly associated with an increased odds of child diarrhea (OR: 1.46; 95% CI: 1.18–1.82, p = 0.001). However, other WASH practices were not found to be associated. The findings underline the dangers of unsafe disposal of child feces and highlight the need for strengthening the related policies and program strategies and their implementation.