The concept of assessing benthic biogeochemical standing stocks as an ecologically relevant parameter has been challenged by one of a dynamic nature: in sands, low standing stocks may mean low carbon burial efficiency due to rapid turnover aided by advective interfacial flows. This concept suggests that a large, diverse and very adaptable population of microbes is present in sands, and that these have a previously unforeseen biogeochemical importance. This view has profound consequences for the scientific outlook on the ecological role of permeable sediments and on the methodological strategies used in the study of coastal ecosystems. Based on a review of the current literature and results gathered at a coastal setting, progress within this new paradigm is examined and underlying questions are speculated upon. The evidence so far shows that, in permeable sediments and at timescales of seconds to a few hours, the dynamics of advective flow to a large extent control microbial diversity, the rates of microbial processes, the size of organic and inorganic pools, and even their respective changes. The importance of obtaining further information on the microbial diversity, the structure of different communities present in sands and their link to biogeochemical function arises from recent field studies. What is also clear from the available evidence is that only a combination of different techniques and approaches, some of which are under development on the fringes of previously almost water-tight research areas, will further understanding of the important functional role of microbial populations in benthic ecosystems.