Estuarine tidal flat sediments are highly productive and biologically rich ecosystems. Their secondary production provides nutrition to large numbers of migratory bird populations and to commercially relevant shellfish and fish stocks. This high productivity can be driven by a range of organic matter subsidies, including deposited phytoplankton and detritus of both terrestrial and marine origin, macroalgae, seagrasses and/or salt marsh vegetation. In most cases, however, the in situ productivity of microbial biofilms fuels a major part of the secondary production on estuarine intertidal flats. These biofilms are complex consortia of benthic microalgae and heterotrophs embedded in a biogenic polymer matrix. They play key roles in a range of important ecosystem functions, such as sediment stabilization and water quality improvement. Nevertheless, several unknowns still exist about the complex interplay between microphytobenthos (MPB), prokaryotes and benthic invertebrates in microbial biofilms on tidal flats. Nematodes are by far the most abundant metazoans, and are also among the most species-rich taxa in estuarine and marine soft substrates and their biofilms. Their high abundances and generally high biomass turnover rates have caused speculation about their importance in tidal flat sediments. Their grazing and non-trophic interactions with biofilm-forming organisms may affect the activity and community structure of both MPB and of sediment bacteria, and thus probably also affect some of the ecosystem processes mediated by these micro-organisms. In addition, nematodes can be an important food source for higher trophic levels. Thus, nematodes may represent an important trophic link between biofilm-forming organisms and higher trophic levels. Moreover, the high local-scale species diversity of nematodes has puzzled ecologists for decades. Differential resource use is often invoked as a basis for niche differentiation among species, yet the vast majority of studies demonstrating that this would be prominent in marine nematodes are based on laboratory experiments on single species or on highly simplified assemblages, leaving the issue of resource differentiation under natural conditions rather understudied until present.