The negative effects of quartz on biological systems are well known, from a clinical point of view, since the XVIII century, anyway the influence of quartz on the marine benthic organisms and communities is underestimated. Interactions between organisms and minerals (biomineralogy) could play a major role on the life cycle of a species and on the spatial distribution and structure of marine and freshwater benthic communities. Various biosystems, at different levels of complexity (cell, organism, species, and community) show, in fact, the ability to recognise, select, react, and possibly use the mineral fraction. A negative influence of quartz on the biological activity has been demonstrated, due to the toxic activity of the silanolic radicals on the surface of the crystalline quartz, which interferes with animal metabolism. The aim of this paper is to review the selective response by benthic organisms to the quartz presence and evaluate the primary role of quartz in affecting the development, settlement and growth of many species. Such selectivity may cause spatial anomalies in species composition, diversity and biomass in marine and freshwater communities and, consequently, have important consequences on basic and applied ecology.