A reverse configured flow injection system was developed for the determination of copper in water samples. In this study, a bathocuproine disulfonic acid copper complexing reagent was used. In the presence of a reducing agent (hydroxylamine), the formation of complex was monitored at 484 nm. The determination range extended from 1 to 40 µg L−1, with an applicable determination rate of 40 h−1. The developed method was applied to the determination of copper in water samples (estuarine, river, and drinking water) and showed good accuracy (z-score below 2). The detection limit of 0.7 µg L−1 copper is consistent with the requirement of the target water samples. The developed method was also used for the comparison of different spectrophotometric flow cells. Alternative flow cells (U, Z shaped, and the liquid waveguide capillary cell) were compared in terms of their sensitivity and response to refractive index changes.