Front-side connected, N-channel, normally-off, SiO2/Si3N4 chemical field effect transistor (ChemFET) microsensors have been fabricated using a standard P-well silicon technology. These ChemFETs microsensors were adapted to ammonium ion detection thanks to photosensitive polysiloxane (PSX) polymer containing nonactine as an ionophore. The ammonium-sensitive membrane has been deposited either manually by micropipette, either by spin coating and patterned using photolithography technique. Both processes have been studied and compared through the ammonium ion determination. The manually deposed layers have been characterised by thickness non-reproducibility. Therefore, spin-coated layers have good reproducibility, but their thickness of 30 µm has been responsible for an increase of the ISFET threshold voltage and a decrease of its bias current. Nevertheless, in both cases, good sensitivities have been shown on the [1 – 5] pNH4 range even if saturation phenomena have been evidenced for the lowest concentrations. These pNH4-ISFETs microsensors are developed for the monitoring of environmental pollution and more precisely for ground water analysis.