(1) Although suffers from intense pollution inputs, Guanabara Bay, the most socioeconomically and environmentally important estuary in Rio de Janeiro, Brazil, is still home to a diverse fauna, including several fish and crab species consumed by humans. The bay presents high sedimentation rates and sediment contamination, further aggravated by dredging processes carried out in recent years. In this context, this study aimed to verify the effect of the dredging process on total mercury (THg) concentrations at Guanabara Bay through swimming crab assessments sampled before (2016), during (2017), and after (2018) the dredging process, and mainly, if the detected concentrations can be harmful to consumer health; (2) Methods: Swimming crab samplings were carried out at the same time and sampling points in 2016, 2017 and 2018 and the total Hg was determined using a Direct Mercury Analyzer (DMA-80, Milestone, Bergamo, Italy); (3) Results: Increased Hg concentrations were observed during the dredging process, decreasing to lower values, close to the initial concentrations, at the end of the process. Some of the investigated abiotic factors favor Hg dynamics in the aquatic environment, while others were positively altered at some of the assessed sampling areas at the end of the dredging process; (4) Conclusions: Although crab Hg levels were below maximum permissible limits for human consumption, it is important to note that these animals are significantly consumed around Guanabara Bay, which may lead to public health issues in the long term.