This document specifies the communities and ecosystems to be studied, as well as the parameters and effects to be analysed and the general methodology to be used. Although the consequences of significant pollution appear in the marine environment as changes of most characteristics of the ecosystem, this manual is mainly providing methods for the assessment of pollution-induced modifications as shown in the structure, and particularly in changed diversity, of communities. The manual recommends that such investigations be focused on benthic communities, combined with as much information as possible on pelagic environmental conditions, bioproductivity and communities. Therefore, basic methods for sampling, processing and determinations of phyto and zooplankton are given as well.