Catchment microbial dynamics is an emerging discipline driven by the demands of catchment scale legislation designed to deliver good water quality and ecosystems. The driver in the EU is the Water framework Directive and its daughter directives which have many parallels in the earlier Clean Water Act in the USA. Both require management of catchment systems to deliver effective protection of receptor sites through programmes of measures in the EU and total maximum daily load (TMDL) investigations in the US. The result of this imperative better to understand the catchment scale drivers of microbial impairment of recreational, drinking and shellfish growing waters has focused attention on: (i) the balance between point and diffuse source pollution inputs; (ii) indicator pathogen relationships particularly the enteric viruses and molecular measurement tools; (i) the novel tracking of pollution to animal and human sources, (iv) the modelling and prediction of pollution loadings both to inform remedial measures design and to offer real time health protection. This contribution seeks to provide a critical assessment of these emerging issues from the perspective pf water and ecosystem managers and regulators drawing on a series of empirical research studies in Europe.