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The analysis of socio-ecological systems requires new, qualitatively different evaluation schemes that enable an integrated assessment of ecological, social, and economic factors through the use of appropriate indicators. This paper addresses the risk assessment of negative impacts from tourism pressure for 10 socio-ecological systems in the Salento region of southern Italy. Two models are combined to perform the assessment. The first is Holling's conceptual sustainability model, which is proposed as an alternative to Butler's Life Cycle model. The second is a fragility model, where fragility is modelled as resource value combined with stress (pressure). Pressure is the number of tourists in each sub-region, and resource value is the proportion of protected area that draws tourists to a sub-region. In this way, the fragility model has a combination of socio- and ecological terms. A new approach is developed to improve the estimates of pressure and fragility, and to provide relevant operational indicators. The number of official (counted) tourist visits generally underestimates the true number of visits, but the discrepancy varies among sub-regions. In order to estimate underhand (uncounted) tourist visits, a separate procedure relating “number of people” to “solid urban waste production” is developed, and then it is used to correct the official estimates. The results suggest that relative risk of sub-regions from tourism pressure may not be adequately represented by official counted visits. The set of developed indicators allow identifying two specific sub-regions as the highest risk areas, and these are discussed in terms of Holling's sustainability model.