Currently, a major challenge on producing high-quality drinking water is to monitor pathogens, such as Giardia, Cryptosporidium and enteric viruses. Due to limitations of the analytical methods available to detect pathogens in water, the research of surrogate indicators is an up-to-date subject. In view of these aspects, a pilot scale study was performed to evaluate the association between microbiological and physical indicators and the presence of Giardia spp and Cryptosporidium sp in the effluent of upflow and downflow slow sand filters. The results showed that efficient bacterial removal could indicate suitable protozoa removal. Although coliforms and Escherichia coli do not present the appropriate physiological profile for an "ideal" indicator, they are still good references for drinking water microbiological quality, specifically for slow sand filtration. The results also point out to the need of deeper researches about the use of anaerobic spores as routine indicator. Regarding the control of Cryptosporidium outbreaks, the expectation that a single indicator will satisfy all purposes is unreal. It may be more useful to know the advantages and disadvantages of several indicators, and integrate them appropriately.