The Mackenzie River Delta is a major outlet to the Arctic Ocean, an important habitat for freshwater organisms, migratory birds, and mammals, and a critical economic and social resource for the Gwich'in and Inuvialuit people. The Delta is also sensitive to climate change, with an increased likelihood of more variable discharge and rising sea levels, leading to forecasts of increasing isolation of many high-elevation floodplain lakes and increasing connectivity of low-elevation lakes. While extensive and ongoing studies of the biogeochemistry of these lakes exist, lower secondary producers such as macroinvertebrates represent an overlooked element of the Mackenzie Delta ecosystem. The objective of this thesis is to identify the effects of flooding on the limnology and benthic invertebrate ecology of this climate-sensitive Arctic region. This thesis addresses this knowledge gap by examining responses of lake water chemistry (Chapter 1) and littoral benthic invertebrates (Chapter 2) to variation in peak flooding, in addition to examining patterns of metacommunity structure across lakes with differing connectivity to the river (Chapter 3). Using a five-year time series that captured recent extremes in peak flood level, I found that connection time was a dominant factor influencing lake water chemistry because of direct flooding inputs and the effects of spring flooding that carried forward through the growing season. The response of lake chemistry to differing annual peak flood levels differed according to the flooding regime of the lakes. Benthic invertebrate communities sampled over five years in the East Channel were also significantly related to connection time and several of the identified water chemistry variables, indicating that they are sensitive to alterations to flooding hydrology. Analyzing the metacommunity and functional structure of macroinvertebrate communities suggested that the hydrological diversity of lakes contributes to the regional diversity, with aquatic dispersers more limited by dispersal opportunity than aerially dispersing insects. These results suggest the promise of further study of benthic macroinvertebrates in this rapidly changing Arctic delta, the importance of considering habitat diversity for freshwater conservation, and the potential for environmental change in response to climate change in north-flowing northern freshwater systems worldwide.