The tank-based irrigated agricultural system in the Dry Zone of Sri Lanka is one of the oldest historically evolved agricultural systems in the world. The main component of the system consists of a connected series of man-made tanks constructed in shallow valleys to store, convey and utilize water for paddy cultivation. Up to 10,000 tanks originating from the heydays of ancient kingdoms are still integrated in the current agricultural landscape. During the last two millennia, this indigenous system has undergone many changes in technological, management and socio-cultural norms. This research aimed to analyze the current management practices and existing indigenous aspects of the Dry Zone irrigated agricultural system from the viewpoint of farmers who are the main stakeholders of the system. Altogether, 49 semi-structured interviews were conducted in seven villages in the Anuradhapura district and a detailed survey was conducted in the village of Manewa with a mixed research approach. The basic elements of the indigenous landscape, agricultural practices and management structures based on Farmer Organizations were mapped and examined in detail. The analysis of results shows that the sustainability of the indigenous agricultural system is vulnerable to rapid changes due to modernization, market changes, education levels, and inconsistent management decisions. The case study demonstrates the value of preserving indigenous agricultural systems and the negative outcomes of current management interventions that neglect the indigenous system. Therefore, careful interventions and innovations are needed to adapt the tank-based indigenous agricultural system of the Dry Zone of Sri Lanka so as to preserve ecological and socio-economic sustainability.