Larval development of the Mediterranean mussel Mytilus galloprovincialis is a well-established model to assess the effects of environmental stressors on marine invertebrates. However, the scarce understanding of the processes regulating larval development in bivalve mollusks prevents the comprehension of their modes of action in these organisms. Accordingly, we devised live staining, whole mount in situ hybridization (WMISH) and immunostaining protocols to investigate in detail shell biogenesis and neurogenesis. These two major morphogenetic processes characterize M. galloprovincialis larval ontogeny and are extremely susceptible to both environmental contaminants and global change. Larval shell biogenesis was studied at close times post fertilization (pf) starting by the early trochophore stage (24 hours pf) until the D-Veliger stage (48 hours pf) with the two live dyes Calcofluor and Calcein which, respectively, stain the organic and calcified portion of the growing shell. During the same developmental window, early neurogenesis was studied with antibodies against the neurotransmitters serotonin (5-HT) and γ-aminobutyric acid (GABA). In addition, WMISH was performed to study the onset of dopaminergic (DOPA) neurons and the global neuronal population. Our results show that shell biogenesis starts at the trochophore stage with the secretion of a saddle-shaped organic matrix providing the scaffold for the following mineral deposition. At this same stage, mussel larvae already present a copious neuronal population which include both 5-HT and GABA positive cells, while DOPA neurons only appear at later stages. In D-Veligers, the shell is D-shaped with the organic and inorganic layers growing at the same rate while neurons, especially 5-HT, are organized in protoganglions. These techniques and findings allowed us to demonstrate neurotoxic as well as direct effects on the early stages of shell biogenesis for diverse stressors including Endocrine Disruptors.