Toxic nitrogen compounds (ammonium and nitrite) during freshwater fish farming are factors that strongly affect fish farming and its effectiveness. Knowledge of the dynamics of these compounds during fish rearing is essential for fish farmers. Since measuring toxic nitrogen compounds is one of the most important actions in commercial fish culture, a two-part experiment was conducted using a Recirculation Aquaculture System (RAS), in which daily fluctuations of ammonium and nitrite concentrations were determined depending on the biofilter media used and the feeding protocol. The first part of the experiment included an analysis of daily nitrite concentration fluctuations using a submerged (moving bed) biofilter with commercial fittings. Two different feeding protocols were applied in this part: one feeding per day (first stage) and feeding distributed over time (second stage). The second part of the experiment involved an analysis of daily ammonium and nitrite concentration fluctuations using trickling biofilters with commercial fittings and polypropylene agglomerate. A submerged biofilter with commercial fittings was used as a reference. Two different feeding protocols were applied in this part: one feeding per day (first stage) and two feedings per day (second stage). The results show the effect of both the biofilter used and the feeding protocol. Increasing the feed dose with an unchanged filter resulted in higher maximum concentrations of both ammonium and nitrite. Dividing a daily dose into several feedings results in a decrease in the maximum ammonium and nitrite concentration while extending the time when concentrations of ammonium and nitrite in the RAS system are increased.