Pharmaceuticals and personal care products (PPCPs) are contaminants of emerging concern that derive primarily in the water environment from combined sewer overflows and discharges from industrial and municipal wastewater treatment facilities (WWTFs). Due to incomplete removal during wastewater treatment, PPCP impacts to aquatic ecosystems are a major concern. The Great Bay Estuary (New Hampshire, USA) is an important ecological, commercial, and recreational resource where upstream WWTFs have recently been under pressure to reduce nitrogen loading to the estuary and consequently upgrade treatment systems. Therefore, we investigated the distribution and abundance of 18 PPCPs and three flame retardants within the Great Bay Estuary and WWTFs discharging to the estuary to examine how WWTF type influenced PPCP removal. All 21 analytes were frequently detected at μg/L to ng/L concentrations in influent and effluent and ng/kg in sludge. WWTFs with enhanced nutrient removal and longer solids retention times correlated to higher PPCP removal, indicating facility upgrades may have benefits related to PPCP removal. Understanding PPCP fate during treatment and in downstream waters informs our ability to assess the environmental and ecological impacts of PPCPs on estuarine resources and develop mitigation strategies to better protect marine ecosystems from emerging contaminant exposure. PRACTITIONER POINTS: PPCP removal positively correlated with solids retention time and varied by treatment facility and compound. Upgrade of WWTFs for biological nitrogen removal may also increase PPCP removal. Surface water fluoxetine concentrations may present an ecological risk to the Great Bay Estuary.