Holistic indicators such as exergy and ascendency have been widely employed to assess the health of ecosystems given by their structure, function and organization. In this study we calculate the exergy, specific exergy and ascendency for the microbenthic loop that represents a major sub-system within the marine food chain. The analysis of the microbenthic loop investigated in terms of organic matter, bacteria, microphytobenthos and meiofauna reflected changes occurring in the trophic state of benthic ecosystems and provided a tool for comparison between different environments. Temporal and spatial variability of the holistic indicators were evaluated using benthic measures collected at different times for different environments in the Mediterranean Sea. Exergy was strongly correlated with the organic contents of the sediments, and did not provide a useful description of the investigated system. In contrast, specific exergy resulted related to the microbenthic loop structure and complexity while Ascendency mostly reflected its activity and organization. Temporal analysis showed that in natural ecosystems specific exergy and ascendency showed convergence and follow similar seasonal trends. On the contrary in strongly eutrophicated systems an uncoupling between the two indicators occurred indicating a malfunctioning of the microbenthic loop that become strongly dissipative. As a result specific exergy and ascendency calculated within the microbenthic loop appeared to be sensitive to changes in environmental conditions and trophic state and may be proposed as useful tools for the health assessment of marine benthic ecosystems. (C) 2004 Elsevier Ltd. All rights reserved.