The Greenland Sea is an important breeding ground for harp and hooded seals. Estimates of annual seal pup production are critical factors in the estimation of abundance that is needed for management of the species. These estimates are usually based on counts from aerial photographic surveys. However, only a minor part of the whelping region can be photographed, because of its large extent. To estimate total seal pup production, we propose a Bayesian hierarchical modelling approach motivated by viewing the seal pup appearances as a realization of a log‐Gaussian Cox process by using covariate information from satellite imagery as a proxy for ice thickness. For inference, we utilize the stochastic partial differential equation module of the integrated nested Laplace approximation framework. In a case‐study using survey data from 2012, we compare our results with existing methodology in a comprehensive cross‐validation study. The results of the study indicate that our method improves local estimation performance, and that the increased uncertainty of prediction of our method is required to obtain calibrated count predictions. This suggests that the sampling density of the survey design may not be sufficient to obtain reliable estimates of seal pup production.