Coastal ecosystems are ecologically critical habitats that also serve as the key interface between the marine environment and human populations. However, these environments are regularly characterised by poor water quality, which can have profound implications for both ecosystem and human health. Poor water quality can be caused by a range of factors, including stormwater inputs that can include sewage, urban and agricultural run-off, and river outflows. However, traditional measures of water quality are often incapable of precisely distinguishing the origins of contamination, hindering the capacity of environmental managers to resolve the causes of coastal pollution. More modern molecular biological approaches, including Microbial Source Tracking (MST) and DNA sequencing, have recently delivered improved capacity to precisely identify the sources and impacts of coastal contamination. I will discuss our successful application of these approaches within a range of coastal ecosystems, where the causes of poor water quality had remained ambiguous using traditional monitoring approaches. Using MST approaches we could precisely identify the sources of contamination and pinpoint the location of input. Finally, I will introduce our plans to expand the application of these approaches into a mobile laboratory scenario, which will permit near real-time delivery of precise coastal water quality assessment.