A tropical mangrove forest in Northern Peru was studied to determine if physical and biogeochemical characteristics of creek water and subtidal sediments are related to the seasonal hydrological regimes. The results showed that during the dry season, there were greater reducing conditions (Eh) and greater fine particle content (silt and clay) in the subtidal sediments. In contrast, the wet season showed greater dissolved oxygen concentrations in creek water as well as lower total organic matter and chlorophyll-a contents in the subtidal sediments. Carbohydrate and protein concentrations indicated remobilization and degradation of sedimentary organic matter, which were higher during the dry season than in the wet season. The results presented here indicate that changes in the hydrological regime affect the biogeochemical dynamics of mangroves, modulating the sediment redistribution as well as the organic matter deposition and degradation. This research provides insight to the biogeochemical dynamics in Peruvian mangrove sediments which are sensitive to extreme El Niño-Southern Oscillation events and the potential effects of climate change.