Synthetic musk fragrances are used in a wide variety of consumer products and can enter aquatic environments through wastewater effluent. Limited data are available on the distribution and behavior of these chemicals, especially in solid matrices and with respect to use patterns and distribution in the United States. Improving our understanding of the environmental fate of musk compounds has implications for risk assessment of both musks and other emerging contaminants. Although nitromusks are known to be hydrophobic, little attention has been paid to their behavior in sediments. A sediment extraction method using sonication was developed and used to analyze samples from San Francisco Bay. Two nitromusk compounds were measured at low levels, with the highest concentrations found in the southernmost region of the Bay. Samples were also analyzed from a nearby tidal channel fed by a wastewater treatment plant outfall, where nitromusks were found at slightly higher concentrations. A nitromusk metabolite was present at concentrations above its parent compound, suggesting that these metabolites may play an important role in the fate of nitromusk compounds. Concentrations of all three compounds were highest at the earliest of four sampling dates, and a geographic survey of sediments along the tidal channel showed that concentrations decreased rapidly with distance from the outfall and were close to background before the channel reached the Bay. To determine if the same pattern existed in other effluent-fed channels, a second study was performed adjacent to another local wastewater outfall. At this site both nitro and polycyclic musks were analyzed, and concentrations in water and suspended solids were measured in addition to sediment. Nitromusk concentrations were lower than at the first field site, and the distribution pattern was noticeably different. In the sediment, concentrations were lowest adjacent to the outfall and increased with distance both up and downstream. Polycyclic musks were present at much higher concentrations and showed a similar distribution pattern in sediment. Concentrations in suspended solids were highest near the outfall and decreased with distance. Aqueous concentrations generally decreased with distance from the source; however, the pattern was much more complex than the one seen at the first field site. A mass-balance computer model was developed to predict the environmental fate of hydrophobic chemicals in rivers and tidal channels. The model was applied to galaxolide at the second field site in hopes of explaining the chemical distribution pattern seen in the field measurements. The results captured the magnitude and some of the observed concentration patterns, but the model was less successful at matching the detailed distribution. An examination of the contaminant mass flows and dimensionless mass transfer parameters suggests that tidal dispersion, settling, and resuspension are the dominant mass transport mechanisms. An unsteady version of a tidal dispersion model was also developed and applied to a tracer in the same system. The results suggest that sampling at neap tide may be preferable to sampling at spring tide since there is less variation in concentration, and that channel branches play an important role and should be considered in future work. Using the model and dimensionless parameters to evaluate important mass transport mechanisms provides valuable information on which processes and parameters have the largest impact on contaminant fate. These insights can be used to adapt and improve the model and to suggest experimental designs to maximize the benefits of future sampling studies.