Species tolerances are frequently used in multi-metric ecological quality indices, and typically have the strongest responses to disturbances. Usually the tolerances of many species are based on expert judgment, with little support from empirical ecological or physiological data. This is particularly true for fish of Mediterranean-type rivers, in which there are many basin-endemic taxa with little information on basic life history traits. In addition, the apparent tolerance of native Mediterranean freshwater fish species to naturally harsh environments and their short-term resilience may mask responses to man-made pressures. Consequently, we evaluated different statistical techniques and procedures for quantifying Mediterranean lotic fish tolerances and compared expert judgment of species tolerances with empirically determined tolerance values.Weused eight alternative approaches to compute fish tolerance values for the Mediterranean basins of SW Europe. Three types of approaches were used: (1) those based on the concept of niche breadth along an environment/pressure gradient (five models); (2) those based on deviations from expected values at disturbed sites as predicted by statistical models describing relationships between species and environmental variables (generalized linear modelling (GLM) and generalized additive modelling (GAM), two models); and (3) one model based on the relatively independent contributions of pressure variables to the data variation explained by statistical models. Tolerance estimates based on the used/available pressure gradient and the average general pressure value had the highest mean correlations with the expert judgment classification (mean r = 0.4) and with the other approaches (mean r of 0.48 and 0.46, respectively). The high degree of uncertainty in tolerance estimates should be accounted for when applying them in ecological assessments. Results also highlights the need for better designed research to separate effects of natural and disturbance gradients on species occurrences and densities.