ABSTRACT1. Transitional waters are ecotones between terrestrial, freshwater and marine ecosystems, being characterized by high spatial heterogeneity and temporal variability.2. The EU Water Framework Directive (WFD) posed to the scientific community the challenge to classify these ecosystems into a small number of types, while retaining a functional classification of ecosystem types.3. A niche theory approach is proposed to identify the limiting forcing factors organizing biological quality elements, i.e. the limiting niche dimensions.4. The analysis of a macro-invertebrate dataset from published papers on 36 Italian lagoons suggested a two-level typological classification of Mediterranean lagoons.5. Basic ecological theories, such as niche and island biogeography theories, have fundamental implications for the process of developing a typological classification for all aquatic ecosystems, as required by the WFD.

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Phytoplankton populations were investigated weekly at a central station in the Fusaro lagoon (Mediterranean Sea) from

Abstract. Recent observations of physico‐chemical and biological parameters in the Gulf of Naples are summarized. The water masses present within the Gulf during the various periods of the year are described. The temporal and spatial distribution of surface nutrients (N‐NO3, P‐PO4, Si‐SiO4) and chlorophyll a are reported and the areas exposed to local eutrophication are identified. Biweekly sampling at a reference station has permitted us also to identify both phytoplankton and zooplankton seasonal cycles. The morphology of the basin and the uneven land runoff distribution are interpreted as causal to the variability of chemico‐physical parameters and of the associated biological communities, giving rise to two subsystems (coastal and “open water”) within the Gulf.