The perfluorophosphonates (PFPAs) and perfluorophosphinates (PFPiAs) are high production volume chemicals that have been observed in Canadian surface waters and wastewater environments. To examine whether their occurrence would result in contamination of organisms in aquatic ecosystems, juvenile rainbow trout (Oncorhynchus mykiss) were separately exposed to a mixture of C6, C8, and C10 monoalkylated PFPAs and a mixture of C6/C6, C6/C8, and C8/C8 dialkylated PFPiAs in the diet for 31 days, followed by 32 days of depuration. Tissue distribution indicated preferential partitioning to blood and liver. Depuration half-lives ranged from 3 to 43 days and increased with the number of perfluorinated carbons present in the chemical. The assimilation efficiencies (α, 7-34%) and biomagnification factors (BMFs, 0.007-0.189) calculated here for PFPAs and PFPiAs were lower than those previously observed for the perfluorocarboxylates (PFCAs) and perfluorosulfonates (PFSAs) in the same test organism. Bioaccumulation was observed to decreased in the order of PFSAs > PFCAs > PFPAs of equal perfluorocarbon chain length and was dependent on the charge of the polar headgroup. Bioaccumulation of the PFPiAs was observed to be low due to their rapid elimination via metabolism to the corresponding PFPAs. Here, we report the first observation of an in vivo cleavage of the carbon-phosphorus bond in fish, as well as, the first in vivo biotransformation of a perfluoroalkyl acid (PFAA). As was previously observed for PFCAs and PFSAs, none of the BMFs determined here for the PFPAs and PFPiAs were greater than one, which suggests PFAAs do not biomagnify from dietary exposure in juvenile rainbow trout.