Wastewater treatment plants are a critical piece of infrastructure that depend on microbes, both resident and incoming. Incoming microbes can be beneficial but may include parasites that need to be removed. Resident microbes, meanwhile, help break down organic waste. While much is known about bacteria in wastewater treatment plants, eukaryotes are frequently overlooked. Recently, researchers examined the whole microbiome of 10 wastewater treatment plants in Switzerland. They utilized metagenomics to measure which microbes were present and metatranscriptomics to analyze their activity. Bacteria were the most numerous— but eukaryotes, particularly protists, showed the most activity, and there was a surprising number and range of active parasites, which were particularly prevalent in the inflow. Network analysis suggested predation by resident microbes likely helped remove parasites. This study highlights the importance of including both metagenome and metatranscriptome data to capture the full spectrum of microbes in wastewater. The results also revealed information about parasite removal, an important but poorly understood process in wastewater treatment.