The most common and consequently analysed brominated flame retardants (BFRs) are polybrominated biphenyls (PBBs), polybrominated diphenyl ethers (PBDEs), tetrabromobisphenol A (TBBPA), tetrabromobisphenol S (TBBPS), and hexabromocyclododecane (HBCD). As these persistent organic pollutants are widespread in the environment and have a number of harmful effects on human health, the production and use of most has been banned for several years. The aquatic environment is polluted by these compounds through their deposition from the atmosphere, sewage sludge, wastewater treatment plants, and landfills, and higher levels are found in areas with developed industry and agriculture and near landfills. Each compound also seems to show preference for specific compartments of the aquatic environment, i.e. water, sediment, or aquatic organisms, according to their physicochemical properties. The aim of this review was to take a closer look at the analysis of BFRs, as without reliable analysis we would not be able to determine their levels and distribution across the aquatic compartments and assess human exposure and health risks. Particularly worrying are the health risks associated with PBDEs in fish, whose levels generally exceed the permitted values.