The toxicity and modes of action of prioritized flame retardants were evaluated in aquatic organisms. The effects of the organophosphorous-containing flame retardant tris (2-butoxyethyl) phosphate (TBOEP) were measured in Daphnia magna after chronic (21-d) and multigenerational exposure (3 generations) as part of a multi-level biological approach including specific gene transcription measured by qRT-PCR, enzyme activity, and life-history endpoints (i.e., survival, growth and reproduction). The effects of two emerging brominated flame retardants, 1,2-bis(2,4,6-tribromophenoxy)ethane (BTBPE) and 2-ethylhexyl-2,3,4,5-tetrabromobenzoate (EH-TBB) were measured in diet exposed juvenile rainbow trout (Oncorhynchus mykiss) after 48-h and 28-d of exposure. Gene transcription was measured by RNA-sequencing and qRT-PCR at the end of the exposure, as well as specific protein biomarker activity.