The wave of modernization and globalization in the last century has rapidly involved a technological paradigm shift from indigenous irrigation water systems to modern systems in arid regions. Despite interest in the drought resilience of indigenous water systems, the impact of this paradigm shift on drought resilience remains poorly understood because previous studies have focused on fixed irrigation water systems. To fill this gap, we investigated the drought resilience of an indigenous and modern irrigation water system that coexists in the drought-prone Mahaweli H region of the Sri Lankan dry zone. To explain drought resilience, we quantified the historical irrigation system performance (1985–2021) of both water systems using the water duty indicator (i.e., the volume of water required to cultivate a unit land area). The statistical Pettitt test was used to detect significant change points in the time series of water duty, and we divided the time line into few periods based on the change points. Furthermore, a quantitative trend analysis of several socio-hydrological variables and a qualitative analysis of their socio-hydrological backgrounds with triggers of water duty were conducted to explain drought resilience path dependency in modern and indigenous water systems. The results indicated a higher drought resilience is embedded in the indigenous system as the mean water duty increment in drought years compared to non-drought years is 16.4% for the indigenous system and 58.3% for the modern system. In addition, drought resilience pathways that elucidated by water duty change points also demonstrated that indigenous water system features a higher drought resilience compared to the modern water system. The findings of this comparative study can contribute to the design of drought resilience improvement strategies in arid region irrigation water systems in a more comprehensive manner.