A sensitive analytical method based on gas-diffusion flow injection system for ammonium ion determination at trace levels with capacitively coupled contactless conductivity detection (C4D) is described. The effects of the chemical composition of the acceptor stream, operating frequency of the conductivity detector, acceptor and donor flow rates, injected volume, and some potential interferents were evaluated. By injecting 100 µL samples, the analytical method showed linear response for ammonium from 2.0 up to 100 µmol L−1 and a limit of detection of 0.8 µmol L−1 (14 ppb). At a flow rate of 0.10 mL min−1 for the acceptor solution, an analytical throughput of 35 injections per hour was achieved. The new flow injection system was successfully applied for ammonium determination in rainwater from São Paulo city.