Abstract1. Pelagic mucilage aggregates are composed of phytoplankton and bacteria, whilst macro‐ and micro‐phytobenthos and bacteria make up the benthic ones. During the summer of 1991 massive mucilage aggregates, both pelagic and benthic, appeared in the Tyrrhenian Sea, seriously damaging fisheries, tourism and the benthic biocoenoses. Only a few, loose benthic mucilages have persisted during the last decade although the pelagic ones have shown a great resurgence during the last autumn.2. 14C autoradiographies show that the mucilage is photosynthesized and excreted by the micro‐ and macroalgae it contains. The mucilage aggregates are a microecosystem with biological and chemical composition, and a functionality that is different from the surrounding waters. The mucilages cannot be the result of a gelification of the Dissolved Organic Matter (DOM) in the water trapping the free algae present in the water.3. Since 1991 up to the present, variations of Dissolved Inorganic Nitrogen (DIN) and Dissolved Inorganic Phosphorous (DIP) and of their ratio have been observed in the surface waters. These variations could be assumed as the cause of mucilages, however, the mucilage occurrence cannot be directly related to the change of nutrient concentrations and ratios because: i) the higher N/P ratio was persistent also during years without mucilages; ii) nutrients and their ratios have a continuous spatial distribution while mucilages have a discontinuous spatial and temporal distribution. It is suggested that mucilage aggregates are the result of a hyperproduction as a pathological response of the algae to a microbial infection. This hypothesis is also supported by some laboratory experiments.4. The observed trophic changes in the surface Tyrrhenian waters have been related to the Levantine Intermediate Waters (LIW) as they are the main source of nutrients for the surface ones. Data collected from several areas between 1982 and 1998 show that changes in the temperature, salinity and nutrient concentrations and ratios took place in the LIW, so changing the Tyrrhenian climate. Copyright © 2001 John Wiley & Sons, Ltd.