Exposure to the anthropogenic chemicals known as endocrine disrupting compounds (EDCs) may result in negative biological effects. Low levels of EDCs in the environment aggravate the problem as exposure is constant. Urban areas concentrate pollution as greater volumes are released from human activities. Water for public supply is particularly vulnerable as the sewage treatment facilities may not eliminate EDCs. The goal was to assess estrogenicity and effectiveness of removal of phthalates in primary and tertiary wastewater treatment facilities in urban cities in the tropical island of Puerto Rico. A yeast bioassay used to measure estrogenicity showed higher removal with tertiary treatment. However, results in the picomolar range suggest low doses of estrogenic compounds were being released to receiving waters. For the phthalates, solid phase extraction and gas chromatography-mass spectrometry analyses revealed removals ranging from 42.9% to 92.4% with tertiary treatment. More than 90% removal was achieved for benzylbutyl phthalate, dibutyl phthalate and bis-2-ethylhexyl phthalate. However, concentrations ranging from 0.86 to 1.29 ppm for the phthalates in the outflow were detected even at the tertiary waste water treatment plant effluent implying failure of EDC removal. These results can assist managers in evaluating pollution control technologies to ameliorate the impacts of EDCs in the tropics.