This paper combines a risk-based two-stage stochastic robust programming (RTSRP) model into an agricultural-ecological system dynamics (AESD) to conduct agricultural-ecological water resources management. It integrates the chance- constrained programming, conditional risk-at-value, two-stage stochastic robust programming with the AESD model. The RTSRP model improves upon the TSRP model by introducing the risk control measurements. The agricultural-ecological dynamic system (AEDS) model can build water connections amid wheat, field corn, seed corn, economic crops, woodland, meadow, and city greening and farmland shelterbelts. Besides, the ecological service value is transformed into the irrigation benefit of ecological sector to guide water allocation amid sub-ecological sectors at a more applicable detailed scale. It can tradeoff relationships between economic benefit and ecological recovery by formulating two enlarging ecological areas scenarios. The combinations of the RTSRP model and the AEDS model can get optimal water allocation schemes, and simulate future sustainable degree (SD) of optimal water allocation schemes and explore relationships amid water allocation, economic benefit, and SD and risk and robustness of model. It is used to the middle reaches of the Heihe River Basin in China to verify its application. The results show that water allocation schemes have different responses on various risk scenarios. Higher water allocation corresponds to bigger water shortage risk and higher robustness of the model. The economic benefit positive with water allocation is contradictory with SD. Enlarging ecological areas contributes to improvements of economic benefit and ecological recovery, but not the SD under the condition of enough water resources.