Novel methods utilizing liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry were validated for low-level detection of 104 pharmaceuticals and personal care products ingredients (PPCPs) and four alkylphenols (APs) in environmental samples. The methods were applied to surface water, sediment, and mussel tissue samples collected from San Francisco Bay, CA, USA, an urban estuary that receives direct discharge from over forty municipal and industrial wastewater outfalls. Among the target PPCPs, 35% were detected in at least one sample, with 31, 10, and 17 compounds detected in water, sediment, and mussels, respectively. Maximum concentrations were 92 ng/L in water (valsartan), 33 ng/g dry weight (dw) in sediments (triclocarban), and 14 ng/g wet weight (ww) in mussels (N,N-diethyl-m-toluamide). Nonylphenol was detected in water (<2-73 ng/L), sediments (22-86 ng/g dw), and mussels (<0.04-95 ng/g ww), and nonylphenol mono- and diethoxylates were detected in sediments (<1-40 ng/g dw) and mussels (<5-192 ng/g ww). The concentrations of PPCPs and APs detected in the San Francisco Bay samples were generally at least an order of magnitude below concentrations expected to elicit toxic effects in aquatic organisms. This study represents the first reconnaissance of PPCPs in mussels living in an urban estuary and provides the first field-derived bioaccumulation factors (BAFs) for select compounds in aquatic organisms. (C) 2013 Elsevier Ltd. All rights reserved.