Sulfite is known to be harmful to human health and associated to sulfur related environmental effects and ideally should be analyzed onsite owing to its instability. Here we describe an automated, miniaturized, and highly efficient dispersive liquid-liquid microextraction (DLLME) system that seamlessly coupled to a UV-vis spectrophotometer for the trace analysis of sulfite in natural waters. The automated DLLME system was constructed by a single syringe pump that is coupled with a multiposition valve. Nanomolar levels of sulfite could be extracted from natural water samples and injected into the hyphenated spectrophotometer for quantification. The whole analytical procedures, including chromogenic reactions, DLLME, collecting and transferring of microvolume of extracts, and spectrophotometric quantification, were automatically carried out. Key parameters that affect the performance of the method were investigated. The method allows the determination of trace levels of sulfite in the range of 15-1500 nM with a detection limit of 1.2 nM. Good reproducibility and recoveries were obtained by analyzing a series of natural water samples that were spiked with different concentration levels. The method was successfully applied to real natural water samples with satisfactory results. The proposed analytical system is light (3.9 kg), simple to use, able to be applied in the field, and sensitive enough for fresh and saline waters analysis.