As nanomaterials in consumer products increasingly enter wastewater treatment plants, there is concern that they may have adverse effects on biological wastewater treatment. Effects of silver (nanoAg), zero-valent iron (NZVI), titanium dioxide (nanoTiO₂) and cerium dioxide (nanoCeO₂) nanomaterials on nitrification and microbial community structure were examined in duplicate lab-scale nitrifying sequencing batch reactors (SBRs) relative to control SBRs that received no nanomaterials or ionic/bulk analogs. Nitrification function was not measurably inhibited in the SBRs by any of the materials as dosing was initiated at 0.1 mg/L and sequentially increased every 14 days to 1, 10, and 20 mg/L. However, SBRs rapidly lost nitrification function when the Ag⁺ experiment was repeated at a continuous high load of 20 mg/L. Shifts in microbial community structure and decreased microbial diversity were associated with both sequential and high loading of nanoAg and Ag⁺, with more pronounced effects for Ag⁺. Bacteroidetes became more dominant in SBRs dosed with Ag⁺, while Proteobacteria became more dominant in SBRs dosed with nanoAg. The two forms of silver also had distinct effects on specific bacterial genera. A decrease in nitrification gene markers (amoA) was observed in SBRs dosed with nanoAg and Ag⁺. In contrast, impacts of NZVI, nanoTiO₂, nanoCeO₂ and their analogs on microbial community structure and nitrification gene markers were limited. TEM-EDS analysis indicated that a large portion of nanoAg remained dispersed in the activated sludge and formed Ag–S complexes, while NZVI, nanoTiO₂ and nanoCeO₂ were mostly aggregated and chemically unmodified. Overall, this study suggests a high threshold of the four nanomaterials in terms of exerting adverse effects on nitrification function. However, distinct microbial community responses to nanoAg indicate potential long-term effects.