Hydrogels immobilizing nitrifying bacteria with different thicknesses of 0.55 and 1.13 cm (HG-0.55 and HG-1.13, respectively) were produced. It was recognized that the thickness of media is a crucial parameter that affects both the stability and efficiency of wastewater treatment. Batch mode experiments were conducted to quantify specific oxygen uptake rate (SOUR) values at various total ammonium nitrogen (TAN) concentrations and pH levels. In the batch test, HG-0.55 exhibited 2.4 times higher nitrifying activity than HG-1.13, with corresponding SOUR values of 0.00768 and 0.00317 mg-O2/L mL-PVA min, respectively. However, HG-0.55 was more susceptible to free ammonia (FA) toxicity than HG-1.13, resulting in a reduction of 80% and 50% in SOUR values for HG-0.55 and -1.13, respectively, upon increasing the FA concentration from 15.73 to 118.12 mg-FA/L. Continuous mode experiments were conducted to assess the partial nitritation (PN) efficiency in practical applications, where continuous wastewater inflow maintains low FA toxicity through high ammonia-oxidizing rates. With step-wise TAN concentration increases, HG-0.55 experienced a gentler increase in FA concentration compared to HG-1.13. At a nitrogen loading rate of 0.78–0.95 kg-N/m3day, the FA increase rate for HG-0.55 was 0.0179 kg-FA/m3day, while that of HG-1.13 was 0.0516 kg-FA/m3day. In the batch mode, where wastewater is introduced all at once, the high accumulation of FA posed a disadvantage for the FA-susceptible HG-0.55, which made it unsuitable for application. However, in the continuous mode, the thinner HG-0.55, with its larger surface area and high ammonia oxidation activity, proved to be suitable and demonstrated its effectiveness. This study provides valuable insights and a framework for the utilization strategy of immobilized gels in addressing the toxic effects of FA in practical processes.