Estuarine shallow areas and coastal lagoons are known to receive and concentrate multiple inputs, either from land, rivers or coastal areas, being intensively impacted by chemical contamination, namely endocrine disrupting chemicals (EDCs). Despite the ubiquitous coexistence of several classes of EDCs in most of these aquatic ecosystems, there is still limited information regarding their combined effects. Furthermore, given the immediate implications for population dynamics, the available laboratory studies almost invariably focus on very specific life history stages, such as embryonic development or reproduction, thus creating a gap on our knowledge of what happens in between. During this ‘intermediate phase’, the newborn larvae and juveniles face numerous challenges whose outcome may impair reproduction or even survival.