Although the deep seafloor represents the largest biome on the planet, its benthos has remained understudied because of logistical difficulties and the cost of access. Long-term, time-series information is needed to understand the small-scale and inter-annual variations required to build predictive models of ecological processes. In this thesis, we employed three newly developed observatory systems, which coupled in situ imagery with environmental data to examine ecological processes in three deep-sea benthic habitats: 1) Megabenthic surface bioturbation on the upper continental slope (400m depth) near Barkley Canyon, off Vancouver Island, 2) Thermal response in polynoid taxa at Main Endeavour Hydrothermal Vent Field (2,100m depth) on the Juan de Fuca Ridge and 3) Behavioural rhythms and bacterial mat growth in Saanich Inlet (100m), a fjord in southern Vancouver Island. To ensure that the imagery collected was useful for quantitative hypothesis testing by a single observer, we employed a step-wise methodological approach, taking advantage of previously acquired knowledge and, in two cases, the interactive nature of cabled observatories, to tailor the sampling frequency to the variables of interest. The application of a diverse array of image analysis techniques and statistical models, easily extendable to other systems, was also demonstrated. The results obtained while conducting the protocol optimization phase described organism and community level responses to environmental variations. Using a remotely operated camera connected to the NEPTUNE Canada cabled observatory, we estimated that total surface sediment turnover by sea urchins and flatfish, the two most important megafaunal contributors, within the field of view required 93 to 125 days in the absence of phytodetrital accumulations. When employing a camera-temperature array system, the most frequently observed mobile megafaunal species, two polynoid taxa, were not found to exploit the recorded temperature gradients suggesting that they employed a thermoconforming strategy to cope with thermal variability. In the aphotic, mostly hypoxic benthos of Saanich Inlet, strong behavioural entrainment, neither diel nor tidal, was not observed. However, significant changes in species composition and bacterial mat substratum coverage were observed following intrusion of oxygenated waters, a yearly event resulting from specific bathymetric features and oceanographic dynamics of this fjord. A Bayesian approach to data modeling was found to be particularly well suited to protocol optimization purposes as complex models could be more easily and intuitively implemented. The further application of our multi-disciplinary step-wise approach will reduce the time required to approach new ecological questions and improve integration of studies carried in different locations. By carefully choosing ecosystem functions which can be used as indicators of change, the current baseline state of the system can be described. Informed long-term monitoring initiatives can then be implemented in order to quantify global ocean responses to anthropogenic factors such as climate change, resource extraction or eutrophication. / Graduate