The hydroperiod determines the biogeochemical conditions and processes developing in the mangrove soil. Floods control the input of nutrients and the presence of regulators such as salinity and sulfides that, in high concentrations, degrade mangrove vegetation. This work aimed to determine biogeochemical and hydroperiod characteristics in natural and degraded mangrove conditions. Three sampling sites were placed along a spatial gradient, including fringe and basin mangroves with different conditions. Tree characteristics and biogeochemical variables (temperature, salinity, pH, redox potential, sulfides) were measured. The structural analysis indicated two conditions: undisturbed (Rhizophora mangle fringe and Avicennia germinans basin under natural conditions) and disturbed (degraded basin, with standing A. germinans tree trunks). The soil porewater salinity, concentration of sulfides, and temperature were significantly higher, and redox potential lower in the disturbed site. The fringe mangrove was permanently waterlogged with higher tides than the basin mangrove. There were more extended flooding periods on the degraded mangrove due to the loss of hydrological connection with the adjacent water body. Waterlogging in basin mangroves increased soil porewater salinity to 87.8 and sulfides to 153 mg L⁻¹, causing stress and death in A. germinans mangroves. Our results show that the loss of hydraulic connectivity causes the chronic accumulation of salinity and sulfides, with consequences on tree metabolism, ultimately causing its death. It probably also involves the succession in microbial communities.