Change in freshwater availability is arguably one of the most pressing issues associated with global change. Agriculture, which uses roughly 70% of the total global freshwater supply, figures prominently among sectors that may be adversely affected by global change. Of specific concern are small-scale agricultural systems that make up nearly 90% of all farming systems and generate 40% of agricultural output worldwide. These systems are experiencing a range of novel shocks, including increased variability in precipitation and competing demands for water and labor that challenge their capacity to maintain agricultural output. This paper employs a robustness-vulnerability trade-off framework to explore the capacity of these small-scale systems to cope with novel shocks and directed change. Motivated by the Pumpa Irrigation System in Nepal, we develop and analyze a simple model of rice-paddy irrigation and use it to demonstrate how institutional arrangements may, in becoming very well tuned to cope with specific shocks and manage particular human interactions associated with irrigated agriculture, generate vulnerabilities to novel shocks. This characterization of robustness-vulnerability trade-off relationships is then used to inform policy options to improve the capacity of small-scale irrigation systems to adapt to changes in freshwater availability.