The inhibition effect of rapid variations of pH in wastewater on activated sludge was investigated in laboratory-scale sequencing batch reactors (SBR). The toxic influence of pH 6.5 and 8.5 was examined. The experiment with pH 8.5 was preferable to formation of high FA concentration and showed a low risk of inhibition of second step nitrification (conversion of nitrites to nitrates). However, the reactor at pH 6.5 showed inhibition of first-step nitrification (conversion of ammonia to nitrites) caused by FNA formation. High ammonia levels caused a decrease in the overall microfauna population, whereas low–enhanced gymnamoebae, Zoogloea, and Chilodonella sp. population increased after 72 h of inhibition. Destructive acidic pH influence caused sludge washout from the reactor and, therefore, higher organic load on ASP and intensive sludge foam due to Zoogloea higher population.