This study assesses the impact species ecology, fish reactions, and natural behaviour have on visual strip transect counts of deepwater fish carried out with an ROV (remotely operated vehicle). Two terraces and one canyon were visited on the continental slope of the Bay of Biscay. Species such as rabbit fish (Chimaeridae) and North Atlantic codling (Lepidion eques) appear to have avoided the ROV. The vertical distance off the bottom provided evidence that some individuals, in particular slickheads (Alepocephalidae) might have been missed by being above the ROV. GLM modelling showed the importance of depth, current speed, and relative surveying direction on transect counts. Natural and reaction behaviour of deep-sea fish will lead to variable and biased population density estimates.