Herein, we determined the contents of Cu(I), Cu(II), and hydrophobic Cu in natural water using on-site sample treatment, solid-phase extraction (SPE), and inductively coupled plasma mass spectrometry (ICP-MS) analysis. To prevent Cu species changes in the sampling, filtering and preconditioning steps were performed in a closed system using plastic syringes and a disposable membrane filter. Bathocuproin disulfonate (BCS) and ethylenediaminetetraacetic acid (EDTA) were selected as a Cu(I)-selective complexing agent and a Cu(II) masking agent, respectively, whereas ascorbic acid (AA) was used to reduce Cu(II) to Cu(I). Pre-conditioned samples were passed through a hydrophobic SPE column, and the retained Cu species were eluted with ethanol. Subsequently, the eluate was concentrated, and the residue was re-dissolved in 2 M HNO and subjected to ICP-MS analysis. No artificial changes of Cu(I) and Cu(II) species were observed at any time, with the analytical detection limit of total Cu and the blank value equaling 0.0008 and 0.0025 μg kg, respectively. The developed method was applied to real estuarine, riverine, and seawater samples collected in Tokushima prefecture, Japan.