A novel, inexpensive, and sensitive microanalytical system for the determination of total ammonia-nitrogen (ammonia-N) in water was developed. The system was designed to detect ammonia using an in-line purging system coupled with a newly designed gas converging flow cell incorporating in-line paper-based colorimetric detection. The gas converging flow cell served as a gas chamber, a paper-based device holder, and a color detection cell. The paper-based device was impregnated with butterfly pea extract (a natural acid-base indicator), the color of which changed on the basis of the generated ammonia gas. Analytical parameters such as concentration of natural indicator and purging time were studied and optimized. The color image could be captured by an integrated endoscope camera or smartphone and analyzed by ImageJ software in RGB mode. Under optimal conditions, two linear dynamic ranges were observed. By using 1:2 (v/v) diluted 2% (w/v) butterfly pea extract in Milli-Q water, a low linear concentration range of 0.05–0.9 mg L−1 with a limit of detection (LOD) of 0.02 mg L−1 and limit of quantification (LOQ) of 0.05 mg L−1 was achieved. By using a non-diluted 2% (w/v) butterfly pea extract, a high linear concentration range of 0.5–4 mg L−1 with an LOD of 0.1 mg L−1 and LOQ of 0.3 mg L−1 was obtained. Finally, the optimized method was leveraged to determine ammonia-N in various water samples from shrimp farming.