The predictable water shortage crisis is intensifying due to frequent extreme weather caused by climate change and human activities. Motivated by urgent practical needs of more scientific and balanced river basin water resources allocation (RBWRA) schemes, a comprehensive bi-level multi-objective programming (BLMOP) model for RBWRA considering uncertain risks and water market is constructed in this paper, which pursues the objectives of environmental protection, equality, and economic development. River basin authority, as the leader of RBWRA, is committed to reducing pollutants while introducing Gini coefficient to maintain the equality of economic development between sub-areas. Meanwhile, the sub-areas (i.e., followers) are dedicated to improving the economic benefit. In addition, the water market is introduced as water redistribution mechanism and its effect is probed into in detail. Moreover, conditional value-at-risk (CVaR) constraints are integrated into the model to control the economic loss caused by the risks of uncertain water availability. To solve the BLMOP model, a novel bi-level interaction based adaptive global equilibrium optimization (BI-aGEO) approach is proposed, which can obtain the best equilibrium solution that satisfies all decision-making participants. Furthermore, the proposed model and approach are applied to the Hanjiang River Basin in central China to elaborate on their feasibility and effectiveness. Results show that the proposed model is effective in ensuring the sustainability, equality and efficiency of RBWRA. The introduction of water market is shown to be able to improve water efficiency and promote water conservation and CVaR constraints play a significant role in controlling economic risks. Finally, some managerial suggestions are provided for different RBWRA participants for more scientific and effective integrated water resources management (IWRM).