Traditional faecal indicator bacteria such as faecal coliforms, Escherichia coli and enterococci have long been used as indicators of faecal pollution in environmental waters. However, the reliability of these traditional indicators has been questioned in terms of their ability to predict the likely presence of pathogens. Another limitation of these indicators is that they cannot be used to distinguish the sources of faecal pollution which need to be known to ensure the improved management of water quality and the assessment of health risk. In recent years, the use of alternative microbial faecal indicators such as faecal anaerobes (i.e. Bacteroides spp., Bifidobacterium spp., Clostridium perfringens), and viruses (phage), and chemical indicators (i.e. faecal sterols, caffeine, and optical brighteners) has become popular because these can provide sensitive and accurate measurement of faecal pollution in environmental waters. In this paper, the advantages and limitations of using alternative indicators for predicting the sources of faecal pollution are briefly evaluated. The correlations between alternative indicators and pathogens in environmental waters are discussed. A combination of traditional indicators along with alternative indicators and markers is suggested for monitoring faecal pollution, and future research directions for direct pathogen monitoring are also discussed.