Research on the toxicity of carbon nanotubes has focused on human health risks, and little is known about their impact on natural ecosystems. The ciliated protozoan Tetrahymena thermophila has been widely studied by ecotoxicologists because of its role in the regulation of microbial populations through the ingestion and digestion of bacteria, and because it is an important organism in wastewater treatment and an indicator of sewage effluent quality. Here we show that single-walled carbon nanotubes are internalized by T. thermophila, possibly allowing the nanotubes to move up the food chain. The internalization also causes the protozoa to aggregate, which impedes their ability to ingest and digest their prey bacteria species, although it might also be possible to use nanotubes to improve the efficiency of wastewater treatment.