Environmental factors are very influential in the transmission of helminthiasis. This study aimed to determine the prevalence of helminthiasis in primary school-aged children living in villages with coastal ecosystem types in Kusan Hilir Sub-district, Tanah Bumbu District. Furthermore, we ought to identify and compare the characteristics of settlement areas that may increase the risk of transmission. This cross-sectional study was conducted in February of 2016 with three sampling areas selected purposively (Sepunggur, Juku Eja, and Sungai Lembu Village). Prevalence of helminthiasis was determined by examination of stool samples from primary school-age children (6-15 years old in Indonesia) in selected villages. Characteristics of settlements observed were settlement density, permanence of buildings, availability of public toilets, and the physical environmental characteristics of soil types. Prevalence of helminth infection were as follows: Juku Eja Village (82.93%), Sungai Lembu Village (24.44%), and Sepunggur Village (6.04%). Helminth species found were varies from Soil Transmitted Helminth (STH) to non-STH groups. Juku Eja Village has the most settlement characteristics that support the transmission of helminth. In order to decrease the risk of transmission, it is crucial to improve the infrastructure of villages such as paving, providing public hand-wash facilities, warning sign persuading not to defecate on the beach, and construction of clean green open space as a playground for children. Mass drug administration for the population needs to be done along with health monitoring (especially helminth infection in children) on an ongoing basis.