Design conditions for marine structures are typically informed by threshold-based extreme value analyses of oceanographic variables, in which excesses of a high threshold are modelled by a generalized Pareto distribution. Too low a threshold leads to bias from model misspecification, and raising the threshold increases the variance of estimators: a bias–variance trade-off. Many existing threshold selection methods do not address this trade-off directly but rather aim to select the lowest threshold above which the generalized Pareto model is judged to hold approximately. In the paper Bayesian cross-validation is used to address the trade-off by comparing thresholds based on predictive ability at extreme levels. Extremal inferences can be sensitive to the choice of a single threshold. We use Bayesian model averaging to combine inferences from many thresholds, thereby reducing sensitivity to the choice of a single threshold. The methodology is applied to significant wave height data sets from the northern North Sea and the Gulf of Mexico. © 2016 Royal Statistical Society