This paper presented the fabrication and calibration of a clad-modified evanescent based plastic optical fiber (POF) sensor for the detection of ammonia in both stagnant and dynamic aqueous media. This optochemical sensor was based on Oxazine 170 perchlorate (sensing material) and polydimethylsiloxane (PDMS) (protective material) thin layers. A special chemical solution was developed for the etching removal of cladding and a methodology for trapping moisture was exercised. Experimental results on dissolved ammonia detection exhibited short response time (≤10 s), low detection limit (minimum detection limit 1.4 ppm), high sensitivity, and excellent reversibility (over 99%).