Lake Whitefish are an ecologically, economically and culturally important fish species in the Laurentian Great Lakes. Although much research has been conducted on spawning-phase adult Lake Whitefish, little research has paid attention to the ecology of larval Lake Whitefish, especially in the source waters of Bruce Nuclear Generating Station. This PhD thesis incorporates key ecological and methodological uncertainties into understanding the effects of environmental conditions on the ecology of larval Lake Whitefish at Douglas Point, Lake Huron. The result is a set of novel ideas and the development of novel methods to help answer this question. Chapter 2 investigates the effects of environmental conditions on the distribution and abundance of zooplankton as a necessary first step in understanding the ecology of larval Lake Whitefish. Chapter 3 evaluates the consistency between DNA barcoding and visual identification methods using a case study of larval fish caught in plankton tows at Stokes Bay, Lake Huron. This evaluation strongly supports the use of DNA barcoding in combination with visual identification to improve the accuracy and precision of species identification. Chapter 4 explores genetic haplotype variation of Lake Whitefish from Lake Huron using DNA barcodes from spawning-phase Lake Whitefish collected at 28 sites around Lake Huron during Fall 2012. While this study did not detect any cryptic lineages of Lake Whitefish in Lake Huron, it did reveal the presence of rare barcode haplotypes that seem to be unique to specific sampling sites. Chapter 5 develops a novel, real-time PCR assay to specifically identify Lake Whitefish in larval fish assemblages. This technique can further increase the speed of identification of Lake Whitefish. Finally, Chapter 6 investigates the effects of environmental conditions on the distribution and abundance of larval Lake Whitefish in nearshore embayments at Douglas Point, Lake Huron. Ultimately, the new knowledge of larval Lake Whitefish ecology generated in this thesis should be seriously considered by Canada/Ontario, First Nations and Industry as they work together to evaluate effects of the existing Bruce Nuclear Generating Station, and the Deep Geologic Repository for Nuclear Waste that has been proposed for construction at Douglas Point, Lake Huron.