The common occurrence of human derived contaminants like pharmaceuticals, steroids and hormones in surface waters has raised the awareness of the role played by the release of treated or untreated sewage in the water quality along sensitive coastal ecosystems. South Florida is home of many important protected environments ranging from wetlands to coral reefs which are in close proximity to large metropolitan cities. Because, large portions of South Florida and most of the Florida Keys population are not served by modern sewage treatment plants and rely heavily on the use of septic systems, a comprehensive survey of selected human waste contamination markers was conducted in three areas to assess water quality with respect to non-traditional micro-constituents. This study documents the occurrence and distribution of fifteen hormones and steroids and five commonly detected pharmaceuticals in surface water samples collected from different near shore environments along South Florida between 2004 and 2006. The compounds most frequently detected were: cholesterol, caffeine, estrone, DEET, coprostanol, biphenol-A, beta-estradiol, and triclosan. The concentration detected for estrone and beta-estradiol were up to 5.2 and 1.8 ng/L, respectively. Concentrations of caffeine (5.5-68 ng/L) and DEET (4.8-49 ng/L) were generally higher and more prevalent than were the steroids. Distribution of microconstituents was site specific likely reflecting a diversity of sources. In addition to chemical analysis, the yeast estrogen screen assay was used to screen the samples for estrogen equivalency. Overall, the results show that water collected from inland canals and restricted circulation water bodies adjacent to heavily populated areas had high concentrations of multiple steroids, pharmaceuticals, and personal care products while open bay waters were largely devoid of the target analytes.