Brazil hosts an extensive coastal area, marked by a great diversity of geoenvironments. The present study evaluated the role of geoclimatic factors in the geochemistry of mangrove soils by using wet extractions and several physical and chemical parameters. Soil samples were collected in 11 mangrove forests from NE (n = 94) and SE Brazil (n = 230). Our results show an important effect of the surrounding geology and climate on the geochemistry of the mangrove soils. NE mangroves are dominated by suboxic soils (mean: Eh of +150 ± 174 mV and pH 7.1 ± 0.5, respectively) while anoxic conditions prevail in the SE mangrove soils (mean: Eh −46 ± 251 mV and pH 6.5 ± 0.5). In the NE region, a period of several months without rainfall and high temperatures leads to soil suboxic conditions. Conversely, at the SE coast, the surrounding mountain range contributes to well-distributed rain favoring anoxic conditions. The contrasting geochemical environment caused differences in the geochemistry of elements such as C, Fe, and S. Significantly higher Fe (193 ± 24 μmol g−1) and organic carbon contents (6.9 ± 7.1%) were recorded in the SE coast. The higher organic carbon contents are possibly related to Fe organo-mineral associations. These differences are ultimately associated with the contrasting geological surroundings (crystalline massifs at the SE and the iron poor sedimentary formations at the NE). The higher contents of reactive Fe and organic carbon also triggered more intense pyritization in the SE mangroves (pyritic Fe: 93 ± 63 μmol g−1). Our results demonstrate that climate and geological surroundings create identifiable patterns at a regional level and, thus, studies should take these factors into account on future global modelling approaches.