For the first time the occurrence of 25 organic micropollutants (OMPs) including; 11 personal care products (PCPs), six phthalate ester plasticizers (PEPs) and eight organophosphorus flame retardants (OPFRs) was investigated in 72 water samples obtained from five bays in the Uganda sector of Lake Victoria. In addition, an assessment of the potential ecotoxic risk of the target OMPs to aquatic organisms was conducted. Water samples were analyzed for the target OMPs using gas chromatography coupled with mass spectrometry (GC/MS). All the target PCPs were found in all the water samples with the exception of musk ketone and 2,6-di-tert-butylphenol. Triclosan (89–1400 ng L⁻¹), benzophenone (36–1300 ng L⁻¹), and 4-methylbenzylidine camphor (21–1500 ng L⁻¹) were the most predominant PCPs. All the six plasticizers were found in all the water samples with dibutyl phthalate (350-16 000 ng L⁻¹), and bis-(2-ethylhexyl) phthalate (210–23 000 ng L⁻¹) detected at the highest concentrations. Five OPFRs out of the eight targeted were found in all the water samples. Tricresyl phosphate (25–8100 ng L⁻¹), tris-(2-chloroethyl) phosphate (24–6500 ng L⁻¹) and triphenyl phosphate (54–4300 ng L⁻¹) were the most dominant OPFRs. The highest concentrations of OMPs were recorded in Murchison and Thurston Bays, presumably due to industrial wastewater effluents from the highly industrialized localities of the two Bays. Ecotoxicological risk assessment showed that PCPs (triclosan, musk ketone, and 4-MBC), plasticizers (dibutyl phthalate, bis-(2-ethylhexyl) adipate and bis-(2-ethylhexyl) phthalate) and OPFRs (tricresyl phosphate, triphenyl phosphate and tris-(2-chloroethyl) phosphate) pose a high ecotoxic risk to lives of aquatic organisms (risk quotients, RQ > 1).