Due to global warming, in the northeastern semiarid coastal regions of Brazil, regional and global drivers are responsible for decreasing continental runoff and increasing estuarine water residence time, which promotes a greater mobilization of bioavailable mercury (Hg) and allows increasing fluxes and/or bioavailability of this toxic trace element and an acceleration of biogeochemical transformation of Hg. In this work, an application of dendrochemistry analysis (annular tree rings analysis) was developed for the reconstruction of the historical pattern of mercury contamination in a contaminated area, quantifying chronological Hg contamination trends in a tropical semiarid ecosystem (Ceará River Estuary, northeastern coast of Brazil) through registration of mercury concentration on growth rings in specimens of Rhizophora mangle L. and using the assessment in sediments as a support for the comparison of profiles of contamination. The comparison with sediments from the same place lends credibility to this type of analysis, as well as the relationship to the historical profile of contamination in the region, when compared with local data about industries and ecological situation of sampling sites. In order to evaluate the consequences of the described increase in Hg bioavailability and bioaccumulation in aquatic biota, and to assess the biological significance of Hg concentrations in sediments to fish and wildlife, muscle and liver from a bioindicator fish species, S. testudineus, were also analyzed. The results of this work reinforce the indicators previously described in the semiarid NE region of Brazil, which showed that global climate change and some anthropogenic factors are key drivers of Hg exposure and biomagnification for wildlife and humans. Considering the Hg concentration present in the top layers of sediment (~20 cm around 15 to 20 years) with the outer layers in the tree ring cores and in the sediment’s cores from Pacoti estuary and the Ceará estuary, overall the data indicate an increase in mercury in recent years in the Hg surface sediments, especially associated with the fine sediment fraction, mainly due to the increased capacity of small particles to adsorb Hg. There was revealed a positive and significant correlation (p < 0.05) between Hg trends in sediments and Hg trends in annular tree rings. This shared Hg pattern reflects local environmental conditions. The Hg concentration values in S. testudineus from both study areas are not restrictive to human consumption, being below the legislated European limit for Hg in foodstuffs. The results from S. testudineus muscles analysis suggest a significant and linear increase in Hg burden with increasing fish length, indicating that the specimens are accumulating Hg as they grow. The results from both rivers show an increase in BSAF with fish growth. The [Hg] liver/[Hg] muscles ratio >1, which indicates that the S. testudineus from both study areas are experiencing an increase in Hg bioavailability. Possible climate-induced shifts in these aquatic systems processes are inducing a greater mobilization of bioavailable Hg, which could allow an acceleration of the biogeochemical transformation of Hg.