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Methods are needed to quickly detect a variety of biological agents that may be released into drinking-water supplies through an intentional contamination incident. In the present study, 13 drinking-water samples were collected from 9 treatment plants to assess the variability of recoveries of biological agents by culture- or microscopic-based methods and to determine detections of organisms by quantitative polymerase-chain reaction (qPCR) after ultrafiltration. Two 100-L subsamples were collected at each site during each sampling event: one was seeded in the laboratory with target control organisms; and, the second was used to determine the natural incidence of target organisms and serve as a negative control. Six waterborne biological agents were targeted, including: Bacillus anthracis (using B. anthracis Sterne); Burkholderia pseudomallei (using Bu. cepacia as a surrogate); Francisella tularensis (using F. tularensis Live Vaccine Strain); Salmonella typhi; Vibrio cholerae; and, Cryptosporidium parvum. Ultrafiltration was used to concentrate all biological agents simultaneously. Samples were analyzed by qPCR (except for S. typhi) by cultural methods for bacterial pathogens, and by immunomagnetic separation/immunofluorescence assay (IMS/FA) microscopy for C. parvum. Recoveries of biological agents were affected by a variety of factors, including potential loss of culturability of Burkholderia at lower temperatures, analytical variability of recoveries between replicate samples, and problems with qPCR reagents. Recoveries by culture methods for bacteria and IMS/FA for C. parvum were variable between samples and between some replicate samples, ranging from below detection to greater than 100%. Recoveries were significantly related to water pH, conductivity, and dissolved organic carbon (DOC) for culture methods but not for IMS/FA. Recoveries by qPCR were not calculated because of problems quantifying organisms by qPCR in the composite seed. Organisms were detected after ultrafiltration by qPCR; only one sample for B. cepacia was a false negative by qPCR in regard to the cultural or IMS/FA method. Numbers found by qPCR after ultrafiltration were significantly related or nearly related to numbers found by the culture methods for B. anthracis, F. tularensis, and V. cholerae but not for Bu. cepacia and C. parvum. Includes 13 references, tables.