An intensive benthic monitoring has been conducted on a regular grid covering the intertidal mudflats of the Pertuis-Charentais (Marennes-Oléron Basin and Aiguillon Bay). Samples were taken by foot or by boats during winter, from December 2003 to February 2015 in more than 250 stations every year. The present dataset includes abundances and biomass densities of all mollusc species and principal annelids as well as mean lengths, flesh mass and shell mass when appropriate or available. The dataset has been formatted into a geo-referenced relational database, using PostgreSQL free software. This long-term dataset has supported many studies in link with shorebird and benthic ecology, including ecosystem comparisons with other mudflats in Europe and Africa. Once published, this dataset can again support studies concerning spatial and temporal changes in species abundance, interspecific interactions and spatio-temporal variability of the resource. After presenting the dataset, we will introduce the advantages and opportunities of publishing a datapaper in our research domain and based on previous studies illustrate what can be done from such a dataset.