A flow analysis electrochemical system has been developed, characterized, and optimized for the determination of arsenite (As(III)). Sensitivity was significantly improved by the electrochemical deposition of gold nanoparticles on a dual glassy carbon electrode, which was inserted into a cross-flow thin-layer electrochemical cell. The electrochemical system was linear up to 15 ppb with a detection limit of 0.25 ppb. Gold deposition was evident from cyclic voltammetry measurements, whereas atomic force microscopy and scanning electron microscopy revealed the size and distribution of deposited gold nanoparticles. The size and density of the nanoparticles were related to the gold salt concentration, deposition time, and potential as well as the electrode position. The response to arsenite was directly related to the frequency, increment, and amplitude of the square wave voltammetry as well as the deposition time and potential. Estimated reproducibility was +/-1.1% at 95% confidence interval for 40 repeated analyses of 8 ppb arsenite during continuous analysis. The reproducibility was far superior if the electrochemical reduction of arsenite was performed in nitric acid instead of hydrochloric or sulfuric acid. The electrochemical system was applicable for analysis of spiked arsenic in mineral water containing a significant amount of various ion elements.