The effects of marine fishing activities on benthic habitat and communities have become an important environmental issue. In addition to the direct removal of target species, effects include by-catch, damage to benthic organisms and alteration of habitat structure. The growing number of studies on the impact of fishing on bottom habitats indicates that the effects vary with the physical nature of the seabed and with the local natural disturbance regime. Several studies have been conducted on fisheries by-catch and discards off the south coast of Portugal since 1996. The results provide an idea of the impact on biodiversity: more than 60% of the species caught by the trawl fishery are discarded. The crustacean trawl captures the greatest number of species, probably due to the greater fishing depth range. In April 2004, the manned submersible ‘Delta’ (from DELTA Oceanographics, USA) conducted a sea campaign integrated in the SEMAPP programme (Science, Education, and Marine Archaeology Program in Portugal) to directly observe and assess the biological, geological, and archaeological aspects. A total of 15 dives were conducted mainly near the head and in the flanks inside Portimão canyon, down to 300 m. Observations showed variations in bottom type, the sedimentary framework and biological communities. These dives (150–300 m depth) also revealed a heavily trawled canyon bottom and erosion structures leading to changes in habitat structure and biodiversity. Of special interest was the occurrence of low-relief boulder substrates with relatively high densities of demersal finfish and shellfish. These sites served as a refuge for several species, whose abundance here was greater than on the surrounding areas of fine-grained substrates. Strong marks on the bottom are apparently caused by the doors of the trawl nets. Their impact will be examined in greater detail in future studies.