Since 2011, Syria has been engulfed in a complex conflict marked by both targeted and indiscriminate attacks on civilians and civilian infrastructure. Water infrastructure has been continuously targeted, exacerbating problems with contamination of and access to clean adequate drinking water, and increasing the risk of waterborne diseases. We aimed to determine whether having access to more functional and chlorinated water stations is associated with a reduced risk of waterborne disease in northwest Syria. We examined the effect of functioning chlorinated water stations on the incidence of waterborne disease in 10 districts of Northwest Syria between January 1, 2017, and June 30, 2021, using weekly reported disease surveillance data and data from a water, sanitation, and hygiene (WASH) system evaluation program of the Assistance Coordination Unit (ACU). We ran eight negative binomial models to examine the association between functioning chlorinated water stations and the incidence of four of the five waterborne diseases: acute bloody diarrhea (ABD), acute other diarrhea (AOD), acute jaundice syndrome (AJS), and severe typhoid fever (STF). Dose-response models were used to investigate how the incidence of disease can theoretically be reduced as functioning and chlorinated water stations strategically increase. Compared to areas with lower quintiles of functioning and chlorinated water stations, the rates of the four waterborne diseases were lower in areas with higher quintiles of functioning and chlorinated water stations. Exposure to functioning water stations had a stronger association with lower rates of waterborne diseases than exposure to chlorinated water stations. Dose-response models demonstrate a potential for curbing the incidence of acute diarrhea and acute jaundice syndrome. The results of this study provide an understanding of the effects of water station functionality and chlorination in conflict settings. These findings support greater prioritization of WASH activities in countries experiencing violence against civilian infrastructure.