Storage space allocation and handling operation problems are two main crucial problems in container terminals. Early research efforts, however, are seldom devoted to studying them together. Therefore, this paper considers these two problems simultaneously for outbound containers in rail-water intermodal container terminals (RWICTs), where rail-mounted gantry cranes, inner trucks, and quay cranes are involved. A two-stage problem is proposed: Stage 1 is to determine locations of the containers and reduce the overlapping amount, considering container weight, departure time, destination ports, and containers left from earlier planning periods in railway container yards, according to the locations of containers from Stage 1; and Stage 2 aims at obtaining optimal job sequences of different types of equipment and minimizing makespans of handling operations, considering some operational constraints, particularly rehandling time and inner truck congestion. To solve the problem, a two-stage heuristic algorithm is proposed, where the rolling planning horizon and a new update strategy are introduced. A heuristic algorithm is introduced in Stage 1 and a novel two-layer genetic algorithm is proposed in Stage 2, which introduces proximity principles and the reselection operation. Afterward, the results from Stage 2 are used to resolve the first stage problem, while the problem in Stage 2 is also resolved using the new results from Stage 1. This iterative process continues until there are no more improvements in Stage 1. Finally, the results of the computational experiments indicate that the proposed model and solution approaches are effective and efficient in solving the two-stage problem for outbound containers in RWICTs. INDEX TERMS Rail-water intermodal transportation, storage space allocation, handling operation, two-stage algorithm, container terminal. The associate editor coordinating the review of this manuscript and approving it for publication was Roberto Sacile.