Water conservation in arid and semi-arid regions faces significant challenges due to low and irregular rainfall, worsened by climate change, which negatively affects rain-fed crop productivity. Various techniques, including supplemental irrigation using runoff harvesting ponds, aim to address these issues but often suffer from water loss due to infiltration, influenced by the pond liner type. This study uses a factorial analysis to assess the farmers’ perceptions of four pond sealing techniques. Using the Waso-2 method, a survey conducted in 2022 among 41 rainwater harvesting pond owners across three regions of Burkina Faso revealed that farmers prioritized impermeability and ease of maintenance over cost and availability. Concrete, scoring 16/20, was the most preferred, chosen by over 75% of farmers for its durability and resistance to weathering, despite its high cost. Geomembrane, with a score of 12/20, was valued for its waterproofing properties but had durability concerns. Clay, although cheap and available, scored 8/20 due to poor waterproofing on unstable ground. Bitumen, the least favored with a score of 6/20, was hindered by scarcity and lack of familiarity. To enhance supplemental irrigation in Burkina Faso and similar regions, waterproof concrete or durable geomembrane liners are recommended. Further research into improving bitumen and clay liners is also suggested. These findings provide key insights into farmers’ preferences, offering guidance for developing effective water conservation strategies to boost agricultural productivity and address food security challenges in the context of climate change.