Water scarcity in agriculture has been identified as one of the most prominent threats to the well-being of smallholder farmers. A study looking at factors affecting smallholder farmers resilience to water scarcity using The Five Capitals framework was conducted in Bantaeng District, Indonesia. The data collected were analyzed with a multinomial logistic model to determine which factors of the capitals have an impact on perceived resilience to water scarcity. Natural capital in the form of agroforestry and access to a direct water source, as well as social capital in the form of engagement in social groups are strongest factors increasing resilience to water scarcity. In addition, latent class analysis revealed four hidden subgroups where over half of the farmers (55%) are identified as learners who have strong positive views and attitudes towards ecosystem services. Our study suggests that understanding socio-ecological system, through determining factors contributing to resilience while also recognizing the profiles of smallholder farmers, may provide a baseline for efficient future interventions, as programs or initiatives could be tailored to target the subgroups that benefit most.