Precise prediction of wave energy is indispensable and holds immense promise as ocean waves have a power capacity of 30–40 kW/m along the coast. Utilising this energy source does not generate harmful emissions, making it a superior substitute for fossil fuel-based energy. The computational expense associated with simulating and computing intricate hydrodynamic interactions in wave farms restricts optimisation methods to a few thousand evaluations and makes a challenging situation for training in deep neural prediction models. To address this issue, we propose a new solution: a Meta-learner gradient boosting method that employs four multi-layer convolutional dense neural network surrogate models combined with an optimised extreme gradient boosting. In order to train and validate the predictive model, we used four wave farm datasets, including the absorbed power outputs and 2D coordinates of wave energy converters (WECs) located along the southern coast of Australia, Adelaide, Sydney, Perth and Tasmania. Furthermore, the capability of the transfer learning strategy is evaluated. The WECs used in this study are of the fully submerged three-tether converter type, similar to the CETO prototype. The effectiveness of the proposed approach is assessed by comparing it with 15 well-established and effective machine learning (ML) methods. The experimental findings indicate that the proposed model is competitive with other ML and deep learning approaches, exhibiting considerable accuracy of 88.8%, 90.0%, 90.3%, and 84.4% in Adelaide, Perth, Sydney and Tasmania and improved robustness in predicting wave farm power output.