Urdaibai was declared a Biosphere's Reserve by UNESCO in 1984. Because we observed a high prevalence of hermaphroditism in mussels sampled in Urdaibai in March 2004, we started the present research work in order to determine the presence of endocrine disruptors (EDs) in sediments and to study possible EDs effects on mussels and oysters using gonad index and vitellogenin (VTG)-like protein levels as biomarkers. Samples were collected at five localities in April 2007 and 2008, and in October 2007. Estrogenic hormones were not detected in sediments and levels of bisphenol A and organotin compounds were very low. Alkylphenols were found at moderate levels and showed a time-dependent decrease. Phthalates were found at levels up to 8000 ng/g. High prevalence of oocyte atresia and necrosis occurred in mussels sampled in April. Retarded gametogenesis was observed in an oyster population from a shipyard. Hermaphrodites or alterations in VTG-like protein levels were not found but the high prevalence of histopathological alterations in oocytes is of concern.