This dataset contains the data and R code used in the manuscript: Effect of Upscaling Nature-Based Coastal Protection on Estuarine Biodiversity Using Foreshores and Transitional Polders.The study presents an integrated modeling approach to predict the long-term biodiversity outcomes of nature-based coastal protection schemes in estuarine environments. We employ a Bayesian hierarchical model as a species distribution model to estimate the distributions of plants and benthic animals under varying environmental conditions.The dataset includes:Species distribution data: Observations of benthos and plant species collected from the Western Scheldt estuary, located in the southwestern Netherlands.Environmental variables: Corresponding abiotic factors influencing species distributions.R code: Scripts used for data processing, model implementation, and result visualization.