The European pond turtle is a threatened freshwater turtle throughout its range. The Natura 2000 site “Grande Brenne” which is the subject of the study is located in the center of France in the department of Indre (“Région Centre-Val de Loire”) within the Regional Natural Park of Brenne. This territory is conducive to Emys orbicularis, which lives there in metapopulations occupying networks of ponds. The aim of the study is to quantify how heathland, forest, meadow and crop habitats may create landscape that favor or not the occupation of ponds and/or certain transition dynamics. The macro-ecological scale study uses MacKenzie’s occupancy dynamic models to investigate the relationship between the major terrestrial habitat types present on the site and the occupancy dynamics of this species. A representative sample of 61 ponds monitored for seven years is prospected five times per season to obtain a set of detection histories. The landscape surrounding the sites is characterized by four variables. The results show that the presence of moorlands and forests in the landscape around the ponds seems to favor the occupation of the pond. A colonization scenario between 2011 and 2017 of the southern periphery of the site is suggested. The study allows to consider interactions between the occupation of the species and the terrestrial habitats present on the site. It also shows that it is essential to consider not only the pond ecosystem in the management of European Pond Turtle, but also all the habitats necessary for the development of the species cycle. Eventually, besides emphasizing the interest of integrating landscape analysis through multivariate analysis in the framework of dynamic site-occupancy modelling to gain in genericity, but we advocate also the use of probabilistic sampling designs to allow for statistical inference and get more robust and accurate projections both in space and time.