ecosystems are complex, highly interconnected systems in which organisms interact with their physical environment. often, to simplify our understanding of their function, populations within ecosystems are treated as either spatially ubiquitous or discrete and fail to fully consider the costs and benefits of organism movement within and across ecosystems. this is especially prevalent in considering the ecosystem function of large aquatic systems like lake superior. though most fishes in lake superior are known to exhibit large scale movements to spawn in the fall or spring, the costs and benefits resulting from this interconnectedness and daily behaviours of fish undergoing these movements are poorly characterized. this knowledge gap is due, in part, to limitations of current survey and assessment methods (i.e., mobile down-looking sonar surveys), which are costly, have known biases that underestimate fish populations, and are inadequate for detecting fine scale fish movements. to combat these gaps, i first used a new stationary acoustic platform to improve the accuracy of fish density estimates in the upper water column compared to traditional down-looking surveys and provide insight into ship avoidance behaviours and temporal migration patterns. i then applied this technology to describe inter-annual, regional, and diel differences in fish behaviour across lake superior. finally, i examined the productive lake superior shoals lakemount and found strong evidence of a deep chlorophyll maxima and of diel-vertical migration behaviour in the fish and mysis at the shoals, both of which are key components for evaluating current-dependent hypotheses for elevated shoal production. however, i conclude that this shoal system would benefit from the use of the stationary acoustic platform as the current standard sampling methods were unable to provide substantial direct support for these hypotheses. [...]