This repository contains data supporting the publication, "Detection of viral, bacterial, and protozoan pathogens and microbial source tracking markers in paired large- and small-volume water samples." The dataset comprises qPCR concentrations of microbial targets in paired large volume and small volume samples from field studies and laboratory recovery experiments, as described in the main publication. "Field studies.csv" contains sample data and target concentrations for three field studies, two in groundwater and one in surface water. In the "Groundwater - Private wells (n = 138)" study, large volume samples taken by dead-end ultrafiltration were compared to small volume grab samples. In the remaining two studies, large volume dead-end ultrafiltration and small volume samples were collected synchronously to remove the effect of spatial/temporal heterogeneity during collection. Only the 15 qPCR assays with detections and common to all studies are included. Geographic information is not included to protect the privacy of study participants. "Recovery data.csv" contains laboratory data for large volume and small volume method recovery of three microbial targets (a bacterium, a virus, and a protozoan) at varying initial concentrations."Storage data.csv" contains laboratory data for microbial target decay during storage prior to processing. Liquid small volume samples and large volume ultrafilters were stored at 4 C to simulate normal sample storage and transport conditions. Concentrations of three microbial targets (a bacterium, a virus, and a protozoan) were determined for storage times from 0 to 96 hours.Descriptive data for all microbial targets is provided in "Target data.csv". An explanation of variables (with units) for all data files can found in "Key to variables.csv".