A combined study of extant nannoflora (calcareous nannoplankton/coccolithophores) and microfauna (ostracods, benthic foraminifera) was conducted in summer period between 2001 and 2003 at Kastro and Korthi gulfs, Andros Island (central Aegean Sea). The results of our study showed that the studied three groups can provide evidence of stress on the natural assemblages and therefore can be used as proxies of declining coastal environments. In particular, the existence of coccolithophore communities with low species diversities, high dominance values and the predominance of Emiliania huxleyi with malformed coccoliths indicate unstable environmental conditions. The environmental stress in ostracod assemblages is mainly proved by the decreasing abundances of Xestoleberis spp. specimens. The response of benthic foraminifers was demonstrated by the increase of foraminiferal tests with morphological abnormalities and the replacement of Amphistegina lobifera – an environmental health proxy- by miliolids and small rotalliid forms.