Anaerobic sulfite-reducing and aerobic spore-forming bacteria are used as indicators to verify the reliability of water treatment plant efficiency. The objectives of this study aimed to highlight the more accurate endospore indicator for water treatment monitoring and to select an efficient filtration system in order to detect low amounts of endospores from large volumes. The performance of two different ultrafiltration modules was assessed with two filtration configurations (tangential and dead-end). The Hemoflow™ and the Dizzer® filters present recovery yields of 73% and 77% for 100-liter samples of drinking and sand filtered water, respectively. Both systems enabled detection of endospores at a concentration level of 100 spores in 100 liters, by analyzing the totality of the volume, whereas the standard method did not highlight the presence of spores, analyzing only 100 mL subsamples. In addition, experiments on a sand filtration pilot confirmed that the concentration calculation using the standard method is not reliable, due to extrapolation from the small volumes analyzed. This study highlights that the collection of large volumes using a fieldable dead-end hollow-fiber ultrafiltration system in association with the detection of anaerobic sulfite-reducing spore-forming bacteria is an effective way to monitor drinking water production.