Because Clostridium perfringens spores are both specific to sewage contamination and environmentally stable, they are considered as possible conservative indicators of human fecal contamination and possible surrogates for environmentally stable pathogens. This review discusses the reasons and summarizes methods for monitoring spores in water. Cultural methods are still preferred over qPCR for routine water quality monitoring because of their low costs. Membrane filter (MF) methods are preferred over the more laborious and less accurate most probable number methods. The most commonly used MF media are TSC medium and mCP medium. TSC normally allows higher recoveries than mCP. TSC produces fewer false-positive results than mCP; however, it does produce more false-negatives. Two newer methods have substantial potential, CP Chromo Select agar, which allows better recoveries and greater specificity than mCP, and the Fung double tube method, which creates anaerobic conditions and allows enumeration of colonies in tubes in 5–6 hours. Aerobic spores are not associated with fecal contamination but they can be surrogates for environmentally stable pathogens in monitoring water for treatment efficacy; Bacillus cereus spores are normally measured on nutrient agar by the MF method.