Soil properties and components in mangrove ecosystems influence their geochemical processes and services. Despite the extensive mangrove areas present in Brazil, few studies focusing on these themes are under development. In this sense, this work aimed to investigate the spatial variability in soil attributes and composition, the geochemistry of Fe, and the isotopic characteristics of organic matter in mangroves in Baía de Todos os Santos (Cacha Prego, Ponta Grossa, Ilha de Maré, Pitinga), which constitutes Brazil’s second largest bay. The soils investigated showed spatial and temporal changes affecting their properties (pH, Eh) and composition (TOC, Fe fractions), as well as clear spatial changes in the redox potential values (+30–+188 mV), with higher values in PT. Soil textures ranged from predominantly sandy (CP, PT, PG: sand, >70%) to a finer granulometry (IM: sand, 33–64%). These characteristics influenced Fe partitioning and organic matter content, with higher TOC and pyrite values observed in IM (FeS2: 2720–9233 mg kg−1; TOC: 4.4–6.6%) and lower sulfide values found in PT, mainly in the dry season (FeS2: 85–235 mg kg−1). The soil δ13C and N/C ratios seem to suggest a mixed origin of organic matter.