We compared mercury (Hg) and stable isotopic ratios of nitrogen (δ15N) in a long-lived apex predator, Alligator Gar (Atractosteus spatula), from a coastal region of the Brazos River exposed to high aerial Hg deposition, to an inland population exposed to moderate Hg deposition, in order to test the relative importance of biomagnification through trophic dynamics and aerial deposition rates in an apex predator. We used generalized linear models (GLMs) to examine the effects of fish size (Length, mm) and Region (Inland versus Coastal) on Hg concentration and δ15N. Length had a significant positive effect on both Hg and δ15N. However, after accounting for the effect of Length, both Hg and δ15N were significantly higher in the Inland population (N = 48; mean ± SE = 0.232 ± 0.020 mg/kg ww and 18.8 ± 0.184‰, respectively) than the Coastal population (N = 45; mean ± SE = 0.143 ± 0.012 mg/kg ww and 16.72 ± 0.291‰, respectively). We further estimated probabilities of Alligator Gar exceeding Hg consumption advisory guidelines used by the World Health Organization (WHO) and the United States Environmental Protection Agency (USEPA). WHO and USEPA exceedance probabilities were 0.414 and 0.048 for Coastal, and 0.835 and 0.276 for Inland populations, respectively. However, WHO and USEPA exceedance probability estimates for fish ≥ 2000 mm climbed to 0.747 and 0.146 for Coastal and ≥ 0.999 and 0.559 for Inland populations, respectively. These results suggest that variation in food web dynamics, and resultant impacts on biomagnification, may be a more important driver of Hg uptake in Alligator Gar, when compared to the role of aerial deposition rates. Our results also demonstrate that Alligator Gar often exceed consumption advisory Hg concentrations, particularly in the largest individuals, and that they likely experience some level of reproductive toxicity because of sublethal Hg exposures.