Offshore windfarms are expected to affect substantially the structure and functioning of marine ecosystems. Collision risks for migrating birds and noise impact on marine mammals and fish are issues of major public concern. Less charismatic organisms, however, from marine algae through to benthic invertebrates and demersal fish receive far less attention. We contend that the benthos deserves much greater attention owing to the numerous ecosystem goods and services, such as marine biodiversity and long‐term carbon storage and natural resources (e.g. for fish, birds, mammals, and finally humans), that are intimately linked to the benthic system. The installation and operation of extensive offshore windfarms in shallow shelf seas will initiate processes which are expected to affect benthic communities over various spatial and temporal scales. Extensive baseline monitoring programmes allow observations of structural changes to benthic communities, but this is a post‐hoc approach. To gain a mechanistic understanding of these processes that enables us to explain the observed changes, specific target monitoring and well‐designed experimental studies are required. In this conceptual talk we will discuss specific cause–effect relationships in the marine benthos arising from the anthropogenic activities associated with offshore windfarms. The identification of cause–effect relationships is the prerequisite for an efficient, hypothesis‐driven approach towards the disentanglement of the various effects of offshore windfarms on the marine benthos as well as on the whole ecosystem.