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Optimal sampling strategies are critical for surveys of deeper coral reef and shoal systems, due to the significant cost of accessing and field sampling these remote and poorly understood ecosystems. Additionally, well-established standard diver-based sampling techniques used in shallow reef systems cannot be deployed because of water depth. Here we develop a Bayesian design strategy to optimise sampling for a shoal deep reef system using three years of pilot data. Bayesian designs are generally found by maximising the expectation of a utility function with respect to the joint distribution of the parameters and the response conditional on an assumed statistical model. Unfortunately, specifying such a model a priori is difficult as knowledge of the data generating process is typically incomplete. To address this, we present an approach to find Bayesian designs that are robust to unknown model uncertainty. This is achieved through couching the specified model within a Generalised Additive Modelling framework and formulating prior information that allows the additive component to capture discrepancies between what is assumed and the underlying data generating process. The motivation for this is to enable Bayesian designs to be found under epistemic model uncertainty; a highly desirable property of Bayesian designs. Our approach is demonstrated initially on an exemplar design problem where a theoretic result is derived and used to explore the properties of optimal designs. We then apply our approach to design future monitoring of sub-merged shoals off the north-west coast of Australia with the aim of significantly improving on current monitoring designs.