The Neolithic Period (c. 6200 – 4900 BC) in the Struma River Valley led to numerous episodes of cultural diversification. When compared with the neighbouring regions, the ecological characteristics of the Struma River Valley are particularly heterogeneous and the Neolithic populations must have adapted to this distinctive and localized ecological setting. It then becomes reasonable to ask if the evolution of cultural variability in the Struma River Valley was at least partially driven by the ecological setting and differentiation in the evolution of the early agricultural niche. I apply an approach based on niche construction theory and Maxent species distribution modeling in order to characterize the relationship between culture and ecology during each stage of the Neolithic Period in the Struma River Valley and to assess diachronic change. An interpretation of the results demonstrates that the continuous reconstruction of the early agricultural niche allowed for settlement expansion into new eco-cultural niches presenting different natural selection pressures and that cultural change followed. I also found that cultural and historical contingencies played an equally important role on the evolution of populations and that ecological factors alone cannot account for the numerous episodes of cultural diversification that occurred throughout the region.