The broad objective of Trina McMahon's research program is to improve our capacity to predict and model microbial behavior, while searching for novel biologically mediated transformations that can be harnessed for engineering applications, including energy production.​ 

McMahon studies the microbial ecology of both natural and engineered systems using molecular tools to investigate microbial community structure and function in lakes and activated sludge. She also uses high-frequency environmental sensor networks to measure important variables that we know influence bacterial communities and is particularly interested in phosphorus, nitrogen, and carbon cycling in lakes and how this relates to eutrophication and water quality. McMahon and her team use highly resolved time series sampling of multiple lakes, combined with metagenomics and meta-trascriptomics to explore how different lineages of freshwater bacteria contribute to this cycling.

She is also engaged in metagenomic and post-genomic approaches to dissecting the metabolism of bacteria specialized in the sequestration of phosphorus in activated sludge. This information will ultimately lead to the construction of more predictive mechanistic and ecosystem-scale models to describe such processes as wastewater treatment and freshwater nutrient cycling.