Meeting ecological water requirements (EWR) is important for guaranteeing watershed system stability in many arid and semi-arid lands. Rainfall–runoff relationships under the effects of climate change may induce many adverse changes for EWR. Inherent uncertainties in water resources management and potential variations in EWR should both be considered to obtain desired water allocation strategies under changing climatic conditions. In this research, an integrated approach was proposed through incorporation of copula functions and a Markov Chain Monte Carlo (MCMC) simulation into a general chance-constrained programming (CCP) modeling framework. The proposed method was found effective for water resource management with respect to the following: (a) tackling correlated features in watershed rainfall and inflow under climate change based on copula–MCMC simulations, (b) obtaining runoff distributions using the copula sampling method under multiple climate change scenarios, (c) analyzing fluctuations of EWR based on varied monthly flows with consideration of diverse runoff distributions, and (d) obtaining desired water allocation strategies through the developed CCP model with consideration of EWR and water shortage risks. Application of the developed method to water resources management in the city of Dalian (China) indicated that the EWR in the watersheds of Dalian would suffer large variations under changing climatic conditions. Moreover, in comparison with the supply in 2025, the increase of water supply from transferring water from the Dahuofang Reservoir (Hun River) would be 6942–33,772, 6942–25,472, and 2849–14,259 Mt with risk tolerance levels of 20%, 50%, and 80%, respectively.