The objective of this study was to test the hypotheses that (1) assemblages of the same broad group of animals respond in a differential way to different classes of disturbance (i.e. there is not simply a generalised stress response), and that (2) the nature of the response differs according to the environmental conditions that the assemblages normally experience. A series of microcosm experiments was carried out to evaluate the responses of intertidal nematode assemblages to treatments of physical and biological disturbance and organic enrichment. Assemblages from an exposed sandy estuary poor in organic matter and from a sheltered muddy estuary rich in organic matter were compared. Results from univariate, graphical/distributional and multivariate methods of data evaluation generally support our initial hypothesis that nematode assemblages exhibit various characteristic changes when exposed to different types of disturbances. Changes in assemblage structure were revealed depending on the type of disturbance, the initial structure of the assemblage and the morphological and physiological adaptations of the species. For both assemblages, biological disturbance caused the least severe changes in assemblage structure. For the sand nematodes, most extreme changes were the result of organic enrichment, while mud nematodes showed the most intense response to treatments of physical disturbance. Assemblages are most affected by the kinds of disturbances that they do not normally experience naturally.