The purpose of this paper is to test the performance of rapid biodiversity assessment techniques in the lagoonal environment at the pan-Mediterranean scale. The multivariate techniques can produce patterns of lagoonal biodiversity along the Mediterranean. Additionally, it is shown that the polychaete inventory can preferably be used rather than the aggregation of information at the family level for the purposes of rapid biodiversity assessment. These techniques, however, appear to be weak for the environmental assessment because they cannot detect differences between the naturally disturbed and the anthropogenically impacted lagoons. Both taxonomic distinctness indices are found to be robust in providing meaningful results for rapid biodiversity/environmental assessment when the crustacean inventory and the polychaete and molluscan ones are used for the estimation of the average taxonomic distinctness and of the variation in taxonomic distinctness values, correspondingly. Conversely, information on the distribution of the macrofaunal species to the Mediterranean lagoons appears to be inadequate for the needs of such rapid biodiversity assessment at a regional scale. It is suggested that information on ecological convergence of the macrofaunal species would probably provide biodiversity indices with additional power, at least in the lagoonal environment.