We present benthic foraminiferal assemblage data from an exhumed Miocene canyon and fan system from the Tabernas Basin (SE Spain). The presence of good indicator taxa and unique assemblages occupying specific environments allows the distinction of slope, canyon and fan environments within the Tabernas Basin by foraminiferal assemblages alone. Five assemblages are defined on the basis of the occurrence of the indicator taxa. Primary control on the distribution of these assemblages is consistent with trends of physical disturbance and consequent defaunation. Barren samples, which are predominantly found in high-energy parts of the proximal canyon, are recognized as representing recently defaunated substrates (i.e. early successional assemblages). High diversity assemblages containing a high abundance of agglutinated taxa are recognised in the undisturbed slope sequences as being the regional equilibrium ("climax") fauna. Intermediate between these end-members are assemblages with low diversity, dominated by calcareous taxa typically found in the relatively low-energy canyon and fan environments, which are recognized as representing the middle phases of the ecological succession. Two further assemblages, a low diversity assemblage typified by Cassidulina laevigata and Bulimina costata and a very low diversity assemblage dominated (> 10% of all benthic tests) by Globobulimina spp., are restricted to low-energy parts of the canyon and fan, and are absent from the proximal canyon and slope. The composition of these assemblages indicate that nutrient supply/oxygenation is a secondary control on the palaeoecology of the canyon system. A conceptual model for the recolonisation of defaunated substrates in El Buho Canyon is proposed, in which either an oligotrophic climax assemblage or a eutrophic climax assemblage can be achieved at the completion of recolonisation of defaunated substrates, depending on environmental conditions.