Studying and forecasting spatio-temporal evolution of fine particulate matter represents an essential task because it constitutes one of the main risks to human health and to biodiversity. This work aims to propose an integrated approach based on the combination of a multilevel and geostatistical analysis in order to evaluate the net effect of the atmospheric suspended particulate matter concentrations on the biodiversity occurring in Apulia Region (South of Italy) in the last years, considering the influence of meteorological conditions. The empirical results will demonstrate a relationship between biodiversity, particulate matter concentrations and deterioration of air quality. Moreover, the construction of probability maps will allow to identify low or high biodiversity areas within the domain under study. These evidences can support policy makers in planning strategies aimed at protecting environment and public health.