Like many insects, mosquitoes, rely on endosymbionts to grow and develop. These can be acquired from the environment. We used next generation 454 pyrosequencing to discern the whole-body microbiome of the mosquito species Culex quinquefasciatus in various larval stadia and following exposure to common pharmaceutical and personal care products (PPCPs) found in wastewater. PPCP treatments included environmentally-relevant concentrations; 1) a combination of common antibiotics, 2) a combination of mammalian hormones, 3) a mixture of the antibiotic and hormone treatments plus acetaminophen and caffeine and, 4) an untreated control. Within control groups, the predominant families of bacterial symbionts change with each larval instar despite consistent diets and rearing conditions. This trend was also seen in hormone treatments but not in the antibiotic or the mixture treatments. Richness and evenness were reduced in both antibiotic and mixture treatments, suggesting that antibiotics remove certain bacteria or inhibit them from increasing to proportions seen in the control treatment. Interestingly, the mixture treatments had greater richness and evenness compared to antibiotic alone treatments, possibly due to the other contaminants facilitating growth of different bacteria. These findings illuminate the complexity of the microbiome of C. quinquefasciatus and may have implications for more effective control strategies.