The impacts of climate change and increased water use for irrigation make it difficult to manage sustainable water use and food production. Sufficient research has not been conducted on how humans adapt to water risks due to climate change. One of the difficulties in considering adaptation measures is that adaptation actions in one sector conflict with the interests of other stakeholders in the basin and trade-off relationships emerge among various sectors. Here, we examined how an effective adaptation in one sector (agriculture) influences the other (water resources) by calculating the “benefits of agricultural production” and “drought risk” under current and future climate scenarios. We built a framework consisting of two process-based models of hydrology and crop science and evaluated shifting of the transplantation date as a promising measure to avoid the degradation of rice quality in Japan. Shifting the transplantation date had opposing effects on the total yield and quality of rice, with an earlier date increasing the total yield and a later date increasing the quality. Furthermore, an earlier transplantation date reduced the drought risk. Thus, in terms of the preferred adaptation options, total yield and drought were synergistic, whereas rice quality and drought were trade-offs. Our results imply that the current transplantation date has resulted from the farmers’ motivation to maximize total yield, but this motivation may change to other factors, possibly rice quality, due to climate change. Overall, this study contributes to the understanding of how interconnected systems evolve when climate or socio-economic conditions change.