A new high-performance liquid chromatography (HPLC) method has been developed to detect ultra-low concentrations of bisphenol-A (BPA) (below 1 ng/L (ppt)) using column switching electrochemical detection (ECD). The results were superior to those obtained from manual pretreatment procedure with membrane stationary phase. BPA is inherently ubiquitous in the environment, including tools and solvents used for its analysis; to obtain meaningful results, therefore, the concentration of the overall BPA contamination must be below the detection limit for BPA using the analytical system. Therefore, purified water for preparing the standard BPA solution must be filtered with a hydrophobic membrane to suppress BPA background levels of contamination. In addition, we investigated methods for effectively preserving environmental water containing BPA. The addition of a small amount of ethylenediaminetetraacetic acid (EDTA) provided good recovery even after overnight storage. By employing these precautionary measures and procedures to reduce BPA contamination from the analytical procedure, we could accurately determine l(-10) ppt of BPA in environmental water samples using a column switching HPLC system.