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An autonomous batch analyzer (ABA) is described for the measurement of ammonium in natural waters. The system combines previously described batch analysis and continuous flow analysis methods. With its simpler design, the system is robust, flexible, inexpensive, and requires minimal maintenance. The sampling frequency is ca. 8 h−1 and the limit of detection ca. 1 nM which is comparable to the most sensitive flow through or batch analysis methods previously described. Reproducibility is 0.6% (n = 10) at an ammonium level of 200 nM. There are three working ranges: 5–1000 nM, 20–4000 nM, and 0.2–25 μM. In addition, the system produces a calibration curve by autodilution from a single stock standard solution with the same accuracy as traditional manual calibration methods. Representative field data and comparisons with standard EPA methods confirm the utility of the ABA.