This dataset comprises RNA sequences from two well-established aquatic sentinel species, Dreissena polymorpha (a mollusk bivalve) and Palaemon serratus (a crustacean decapod), which are commonly used as bioindicators of environmental health. In addition, the dataset included the prediction of open reading frames (ORFs) of these reference transcriptomes, which can aid in the interpretation of mass spectra during proteogenomic analyses.