This paper presents a systematic methodology to optimise the geometry of a three-body hinge-barge wave energy converter, to maximise the energy extraction of the device in given sea states and in site-specific wave climates. To that end, a 5-degree-of-freedom mathematical model is proposed to describe the system dynamics in two-dimensional space and a two-layer optimisation is designed to find the optimal design and control variables. The inner-layer optimisation is used to find the optimal control parameters of the power take-off system and the outer-layer optimisation, which uses a genetic algorithm, is employed to find the optimal design parameters of barge lengths and of optimal ballast positioning. In the case study, this methodology is applied to a 1:20 scale prototype of the McCabe Wave Pump device. Numerical results indicate that the optimal dimensions of the device, under given sea states, can be found efficiently and accurately, and that there appears to be no obvious benefit in the use of three barges, over a two-barge system.