Physical disturbance is a key factor in controlling the spatial and temporal composition of shallow-water benthic communities. Like shallow waters, deeper waters are increasingly subject to a range of anthropogenic disturbances, which can lead to significant alterations in sedimentation patterns. These alterations often exceed naturally occurring changes. We used a combined analysis of six independent data sets arising from large-scale field surveys and small-scale laboratory experiments to investigate the effects of seabed disturbance on nematode communities. Disturbance response was documented as a function of disturbance type (coastal development, dredged material disposal, bottom trawling, glacial fjord) and intensity (low, medium, high). Natural and man-induced seabed disturbance exerted differential effects on exposed populations, generating changes in the taxonomic (genus) and functional (feeding type) attributes of their assemblages. The genus composition of nematode assemblages from geographically separate seas converged with increased level of various types of man-made disturbance. Assemblages present along a gradient of natural disturbance in a glacial fjord followed an opposite response vector, suggesting that community changes induced by anthropogenic activities, or experimental treatments simulating the principal impacts of these, inherently differ from disturbance of natural origin. Changes in trophic diversity and structure were primarily driven by factors confounded with physical disturbance, such as metal contamination. Coupling the results of analyses at multiple scales proved a useful means of providing deeper insights into the general response of ecological communities to environmental change.