The high production levels of the Chilean salmon farming industry have resulted in the emergence of several diseases that affect all stages of development of cultured species. The parasitic copepod Caligus rogercresseyi is considered a potential vector of pathologies, and different chemical compounds such as pyrethroids and organophosphates have been used to prevent and control sea lice outbreaks. In this study, the effect of azametiphos, deltamethrin, and emamectin benzoate on the larval stages of the mussel Choromytilus chorus and the sea-urchins Sphaerechinus granularis and Paracentrotus lividus was explored. No effects were found in the final larval development of C. chorus (D larvae). However, the trochophore development seemed accelerated in the presence of pesticides compared to the control larvae. In the case of P. lividus and S. granularis, exposure to all pesticides caused an increase in the rate of abnormal larval development compared to the control.