Cyprus is currently the leading country in antibiotic consumption among all European Union member countries and is likely to have a high consumption of pharmaceuticals overall. This reconnaissance type of project sought to investigate the occurrence of 16 pharmaceuticals, six known or suspected endocrine disrupting compounds (EDCs), two flame retardants, one insect repellant, and one fragrance for the first time in water supplies of Cyprus. Groundwater samples from sites that were located beneath farms scattered around Cyprus, wastewater influent and tertiary-treated effluent, raw and finished surface water, and household potable water samples were analyzed using liquid chromatography and tandem mass spectrometry. Most of the tested compounds were < minimum reporting limit, except for ibuprofen (mean of 1.4 ng L−1) and bisphenol A (mean of 50 ng L−1), which were detected in more than one out of the five groundwater sampling sites. Certain compounds were found in large concentrations in the wastewater influent (caffeine 82,000 ng L−1, sulfamethoxazole 240 ng L−1, ibuprofen 4,300 ng L−1, and triclosan 480 ng L−1). However, several pharmaceuticals and EDCs were detected in the tertiary-treated effluent (recycled water). For the raw and finished surface water, and potable water samples, ibuprofen was detected, whereas, bisphenol-A was measured in only potable water. Overall, with a few notable exceptions, source, finished and potable water had rare detection or low concentration of target compounds, but further research is needed to elucidate the temporal and spatial distribution of the detected emerging contaminants along with the characterization of the related public health risk.