The hydrological cycle in irrigation areas under the influence of anthropogenic activities has emerged as a significant topic in the realm of water science research. The southern hilly irrigation area of China, characterized by its undulating terrain and myriad ponds, presents a unique opportunity for water storage and paddy field irrigation. However, these distinct landscape features have also given rise to a complex hydrological cycle with unclear exchange dynamics and a paucity of quantitative calculations on the reuse of return flow. To explore the fundamental laws governing water circulation in irrigation areas, we embarked on in-situ field trials over the 2a period (2021-2022), with the Yang-shu-dang watershed in the Zhanghe Irrigation System of Hubei Province, China, serving as our study area. Our approach entailed monitoring the groundwater depth of 4 typical paddy fields, the water storage levels of 5 typical ponds, as well as the flow of the bucket ditch outlet. The complexity of the hydrological cycle in southern hilly irrigation areas necessitates the development of a novel water balance formula for paddy fields, ponds, and ditches, respectively, that accurately captures their unique features. To this end, we conceived of a method for reviewing the water volume of the source and sink areas in paddy field irrigation water delivery, known as ‘start-to-end comparison’, which enables us to discern the locations in which reuse of return flow is taking place. Through the evaluation of the hydrological cycle and the extent of reuse of return flow during various reproductive stages, we obtained valuable insights into the significant ways in which human activities have disrupted the hydrological balance in southern hilly irrigation areas. The findings of our study revealed several valuable insights. First, the relative error for the 2 a period of paddy irrigation water amount computed by the water balance formula and the DRAINMOD model, as well as the total irrigation water volume from ponds, ditches, and channels were 4.65% and −2.74%, respectively, implying that ‘start-to-end comparison’ is a reliable and robust method that provides a new ideal for irrigation water volume simulation and review in multi-source irrigation areas. Further analysis revealed that the proportion of channel, ditch, and pond sources in different paddy irrigation sources were 9.77%, 71.81%, and 18.42%, respectively. Notably, due to the need for irrigation in paddy fields, 82.73% of initial pond water storage was consumed during whole reproductive stages. Moreover, canal supply, precipitation, and ditch supply accounted for 38.15%, 29.98%, and 14.60%, respectively. It transpired that the late tillering stage featured the highest reuse of water from the pond, with a gradual decline observed during the whole reproductive stage. While both the amount of return flow in the ditch and the amount of reused return flow water increased initially and then decreased, the ditch still emerged as the primary site exhibiting the reuse of return flow, with rates doubling that of ponds (80.86%). We also delved into the consumption pathways of irrigation water after channel irrigation, where in the first distribution of channel irrigation water accounted for only 29.44% into the paddy field. A second distribution facilitated the entrance of at least 72.10% of channel irrigation water into the paddy field. Intriguingly, only 3.44% of the water from channel irrigation was discharged out of the bucket ditch. The remaining 24.46% of the water lingered within the study area, with the potential for subsequent reuse. Examination of the hydrological cycle revealed that the paddy field system was characterized primarily by the vertical movement of irrigation-evaporative transpiration, while the pond system was characterized predominantly by the lateral movement of channel supply-pumping irrigation, and the ditch system was characterized primarily by the lateral movement of paddy drainage-pumping irrigation. Research showed that human activity is the main factor of effect ponds and ditch hydrological cycle. Strategies from irrigation district managers, ‘the main for ponds, the secondary for paddy’ met the needs of farmers and own high irrigation coefficient in southern hilly irrigated area.