Traditionally, Lake Winnipeg fish stocks have been monitored using gillnetting techniques by the Province of Manitoba to collect critical information on fish population estimates, age, and sex ratios. However, gillnetting can be lethal and is often biased towards larger, pelagic, more active, mature, and abundant species. A monitoring technique that does not require the physical capture of fishes is environmental DNA (eDNA). Although eDNA is unable to provide information on the age and sex ratios of Lake Winnipeg’s fish stocks, some studies have shown success in detecting species underestimated in gillnets such as smaller-bodied, less active, immature, less abundant, and benthic species, as well as estimating the relative abundance of species. Therefore, the main goal of my Chapter 2 was to investigate the biases of gillnetting and compare them to eDNA, and how they may be affected by environmental factors for seven species in Lake Winnipeg: walleye (Sander vitreus), sauger (Sander canadensis), yellow perch (Perca flavescens), trout-perch (Percopsis omiscomaycus), spottail shiner (Hudsonius hudsonius), Coregonus spp. (lake cisco (Coregonus artedi), lake whitefish (Coregonus clupeaformis), shortjaw cisco (Coregonus zenithicus), bloater (Coregonus hoyi), and rainbow smelt (Osmerus mordax). My study found that eDNA was able to provide a broader scope of the fish community than gillnetting, especially for rainbow smelt that were detected using eDNA, but none were caught in gillnets. Year was an important factor that affected eDNA presence or absence, but not gillnetting. Environmental factors did not appear to have a greater impact on either eDNA or gillnet presence or absence. In Chapter 3, my research question was to investigate if there was a relationship between gillnetting and eDNA relative abundance estimates. A positive relationship was observed for some models of yellow perch, Coregonus spp., and trout-perch; however, additional research will be required as some models only had a positive relationship for sites across Lake Winnipeg as a whole, but not observed within local groups of sites, or vice-versa.