A new method based on liquid-liquid extraction (LLE) coupled to reverse phase liquid chromatography and atmospheric pressure chemical ionization mass spectrometry (LC-APCI-MS) has been applied to determine trace amounts of caffeine (1,3,7-trimethylxanthine) in surface water samples from a near coastal ecosystem such as Biscayne Bay, Florida. The rational behind the development of such method will be to evaluate the use of unmetabolized caffeine as a potential dissolved phase tracer of human waste contamination. The method allows for the determination of caffeine at levels as low as 4.0 ng/l (ppt) in both salt and freshwater by extracting and concentrating a 1-1 water sample to a final volume of 500 microl and using HPLC separation coupled to an atmospheric pressure chemical ionization mass spectrometry (APCI-MS) system operated in selected ion monitoring (SIM) for the protonated molecular ions (M + H(+)). Samples from different portions of Biscayne Bay and the Miami River, one of its major tributaries, were analyzed and caffeine was detected in those areas previously identified for consistently exceeding the water quality criteria for fecal coliform bacteria contamination. The caffeine concentration in the samples with positive detection was generally low at levels equal or lower than 41 ng/l. However, there is a marked difference between samples collected in open bay areas and those collected from the Miami River.