Quantitative PCR data from mesocosm experiments and field evaluations comparing coarse filter-large water volume environmental DNA samples vs. fine filter-small water volume environmental DNA samples for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. Mesocosm experiments took place at the US Fish & Wildlife Service's Creston Fish Hatchery in Montana, 2016. Field surveys took place in the Flathead River basin of Montana, 2016.