Waterborne autonomous guided vessels (waterborne AGVs) moving over open waters experience environmental uncertainties. This paper proposes a novel cost-effective robust distributed control approach for waterborne AGVs. The overall system is uncertain and has independent subsystem dynamics but coupling objectives and state constraints. Waterborne AGVs determine their actions in a parallel way, while still minimizing an overall cost function and respecting coupling constraints robustly by communicating within a neighborhood. Our first contribution is the proposal of the system robustness level for the cost-effective robust distributed model predictive control (RDMPC) for waterborne AGVs. Cost-effective RDMPC models the price of robustness by explicitly considering uncertainty and system characteristics in a tube-based robust control framework. The second contribution is an efficient integrated branch & bound (B&B) and the alternating direction method of multipliers (ADMMs) algorithm for solving the cost-effective RDMPC problem. The algorithm exploits special ordered variable sets and combining branching criteria with intermediate ADMM results conducting smart search in B&B. Simulation results demonstrate the effectiveness of the proposed approach for cooperative distributed waterborne AGVs with cost-effective robustness.