Mercury concentrations in freshwater food webs are governed by complex biogeochemical and ecological interactions that spatially vary and are often mediated by climate. The Arctic Coastal Plain of Alaska (ACP) is a heterogeneous, lake-rich landscape where variability in mercury accumulation is poorly understood. Earlier research indicated that the level of catchment influence on lakes varied spatially on the ACP, and affected mercury accumulation in lake sediments. This work sought to determine drivers of spatial variation in mercury accumulation in lake food webs on the ACP. Three lakes that were a priori identified as “high catchment influence” (Reindeer Camp region) and three lakes that were a priori identified as “low catchment influence” (Atqasuk region) were sampled, and variability in water chemistry, food web ecology, and mercury accumulation was investigated. Among-lake differences in ninespine stickleback (Pungitius pungitius) length-adjusted methylmercury concentrations were significantly explained by sulphate concentration in lake water, a tracer of catchment runoff input. This effect was mediated by fish growth, which had no pattern between regions. Together, lake water sulphate concentration and fish age-at-size (proxy for growth) accounted for nearly all of the among-lake variability in length-adjusted methylmercury concentrations in stickleback (R²_adj = 0.94, p < 0.01). The percentage of total mercury as methylmercury (a proxy for net Hg methylation) was higher in sediments of more autochthonous, “low catchment influence” lakes (p < 0.05), and in the periphyton of more allochthonous, “high catchment influence” lakes (p < 0.05). The results indicate that dominant sources of primary production (littoral macrophyte/biofilm vs. pelagic phytoplankton) and food web structure (detrital vs. grazing) are regulated by catchment characteristics on the ACP, and that this ultimately influences the amount of methylmercury in the aquatic food web. These results have important implications for predicting future mercury concentrations in fish in lakes where fish growth rates and catchment inputs may change in response to a changing climate.