<p>Coastal waters are the ultimate destination for both point and non-point sources of contamination. The uncontrolled dicharge of fecal waste into the ocean harms natural resources, marine life, and poses health risks to humans. Regular monitoring of coastal water quality and source tracking is important to prevent disease outbreaks. This review discusses all the fecal source tracking (FST) methods, ranging from traditional enumeration techniques to recent next-generation sequencing approaches, in the light of application on coastal waters. The advantages and disadvantages of the individual markers, method comparisons based on performance, correlation of marker with fecal indicator bacteria, and stability under waste water treatment and in field applications are mainly focused on enlightening the “tool box” approach for the marine environment.</p> Graphical Abstract <p>Graphical abstract representing the source and impact of fecal contamination on coastal waters.</p> <p></p>