The increase of stress induced changes in marine environments caused by different types of marine pollution made necessary the search for indicators that assist in assessing pollution effects at the community level. The main goals, with a view to an effective management, are the early detection and evaluation of environmental responses to pollution and to avoid or mitigate negative impacts that different uses may generate. Exergy has been considered as a promising indicator of ecosystem integrity, acquiring a considerable interest in the context of systems ecology. In this research we have tested the capability of exergy (both the exergy index and specific exergy) alongside other diversity indices (Shannon and Margalef indices) of distinguishing organically enriched areas in a Mediterranean coastal lagoon (El Mar Menor). Results show that the exergy index and specific exergy were able to give useful information on community structure, although they were not capable of distinguishing high and poor organically enriched areas or affected by any other type of pollution. Diversity indices were more sensitive to organic pollution. We may say that the exergy and specific exergy are still not applicable as the only ecological indicators in a generalized way in the field of environmental management. Therefore, they still require further application in a wider range of geographical areas and in different conditions in order to study more widely the properties of exergy as an ecological indicator.