The assessment of mercury (Hg) contamination in Peruvian mangrove sediments was conducted across two contrasting environments: the anthropogenically impacted mangrove forest of “Puerto Pizarro” (PP), affected by shrimp aquaculture, mining activities, and urban expansion, and the relatively pristine Mangrove Sanctuary of Tumbes (MS). In PP, Hg concentrations ranged from 291 to 177 ng g⁻1, yielding a Pollution Index (PI) of 1.6 and exceeding the sediment quality guideline defined by the Effect Range Low (ERL; 150 ng g⁻1), indicative of potential Hg toxicity. In contrast, Hg concentrations in MS ranged from 135 to 17 ng g⁻1, remaining below the ERL and within natural background levels reported for Peruvian marine sediments. Using the estimated mean background concentration in MS sediments (70 ng g⁻1), enrichment factors of up to 3.2 were observed in PP sediments. Mercury concentrations in MS exhibited significant positive correlations with fine-grained sediments (silt and clay; r = 0.66) and reactive iron phases (r = 0.70), reflecting natural geochemical controls on Hg accumulation. Conversely, no significant correlations were detected in PP, suggesting that anthropogenic inputs override sedimentological and geochemical processes. This study provides the first assessment of Hg concentrations in mangrove ecosystems located at the eastern South Pacific distributional limit and highlights the role of mangroves as effective biogeochemical barriers that mitigate Hg transfer to adjacent coastal ecosystems.