We developed and validated a microfluidic instrument for interference-free determination of boron in produced water. The instrument uses a boron-specific chelating resin to separate the analyte from its complex matrix. Ten produced water samples were analyzed with the instrument and the results were successfully validated against ICP-MS measurements. Removing interference effects enables precise boron measurement for wastewater even with high total dissolved solid (TDS) levels. 1,4-Piperazinediethanesulfonic acid conditions the resin and maintains the optimum pH for boron adsorption from the sample. Boron is then eluted from the resin using a 10% sulfuric acid solution and its concentration measured with the colorimetric carminic acid assay in 95% sulfuric acid. The use of a microfluidic mixer greatly enhances the sensitivity and kinetics of the carminic acid assay, by factors of 2 and 7.5, respectively, when compared against the same assay performed manually. A maximum sensitivity of 2.5mg(-1)L, a precision of 4.2% over the 0-40.0mgL(-1) measuring range, a 0.3mgL(-1) limit of detection, and a sampling rate of up to four samples per hour were achieved. Automation and microfluidics reduce the operator workload and fluid manipulation errors, translating into safer and higher-quality measurements in the field.