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This chapter focuses on the detection and enumeration topics related to the sanitary microbiology of the receiving waters. The chapter also discusses the examples of alternate indicators. In recent years, the environmental pathogens, such as mycobacteria and Campylobacter , have been the cause for public health concern. Even though clostridia are fermentative saprophytes, they are commonly associated with the food-borne diseases in humans—owing to their ubiquity, the high temperature tolerance of their spores, and their ability to elaborate extremely potent endotoxins. Because Cryptosporidium oocysts are resistant to chlorination, it is suggested that the C. perfringens shouldbe used as an indicator of the drinking water treatment. C. jejuni is most frequently associated with the campylobacteriosis infections in humans. Recovery of cells from the natural waters is hindered by slow growth rates, competitive background microbiota low numbers, and possible non-culturability. Due to the complexities for detection of Campylobacter spp. from environmental samples, many applications of molecular methods based on PCR exist for its detection in poultry, feces, environmental waters, and sewage.