Regions dependent on agricultural production are concerned about the uncertainty associated with climate change. Extreme drought and flooding events are predicted to occur with greater frequency, requiring mitigation strategies to reduce their negative impacts. Multi-purpose local farm water retention systems can reduce water stress during drought periods by supporting irrigation. The retention systems’ capture of excess spring runoff and extreme rainfall events also reduces flood potential downstream. Retention systems may also be used for biomass production and nutrient retention. A sub-watershed scale retention system was analysed using a dynamic simulation model to predict the economic advantages in the future. Irrigated crops using water from the downstream reservoir at Pelly’s Lake, Manitoba, Canada, experienced a net decrease in gross margin in the future due to the associated irrigation and reservoir infrastructure costs. However, the multi-purpose benefits of the retention system at Pelly’s Lake of avoided flood damages, nutrient retention, carbon sequestration, and biomass production provide an economic benefit of $25,507.00/hectare of retention system/year. Multi-purpose retention systems under future climate uncertainty provide economic and environmental gains when used to avoid flood damages, for nutrient retention and carbon sequestration, and biomass production. The revenue gained from these functions can support farmers willing to invest in irrigation while providing economic and environmental benefits to the region.