Eggs from mature Chinook (Oncorhynchus tshawytscha) and Coho (Oncorhynchus kisutch) salmon were collected between 2004 and 2014 from the Salmon River fish hatchery in Altmar, New York. The egg samples were analyzed for seventeen polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), as well as four dioxin-like polychlorinated biphenyls (DL-PCBs) using USEPA methods 1613 and 1668. Salmonid eggs were chosen as a tissue of interest since salmon feed at all trophic levels of the food web as they grow, and spawn in a narrow range of ages providing consistent, representative, and temporal samples of contaminant exposure. First-order decay models indicate decreasing trends for all select contaminants in both species, expressed by a toxic equivalence (TEQ) half-life (t1/2) of 11 years in Chinook and Coho eggs. No significant statistical difference in contaminant elimination rates were noted between species. TEQ elimination rates for Coho and Chinook eggs were not significantly different (p > 0.05) when compared with published Lake Ontario whole-fish lake trout elimination rates. Our research demonstrates that salmonid eggs are an effective means to assess PCDD, PCDF, and DL-PCB exposures and long-term trends in the Great Lakes.