The Southern Everglades mangrove ecotone is part of a highly oligotrophic, P-limited estuarine ecosystem. The wetland vegetation in this region is comprised mostly of dwarf red mangrove spanning the oligohaline zone between the freshwater marshes to the north and Florida Bay to the south. The hydrology of the region is wind and runoff-dominated with a small tidal component and is characterized by a strong seasonal pattern in rainfall and discharge from numerous creek systems. We conducted a two-year study in Taylor River—one of the larger creek systems in this region—to understand seasonal controls on nutrient dynamics along the mangrove ecotone. Water temperature, salinity, pH, and dissolved oxygen were measured hourly during each 7-day sampling period in wet, dry, and transitional seasons. We also sampled surface water nitrogen (total and inorganic) and phosphorus (total and inorganic) every six hours at upstream and downstream locations throughout each sampling. We saw clear seasonal differences in water quality between seasonal samplings as well as between the upstream and downstream ends of this ecotone. Discharge magnitude, wind, and tidal forces had a strong influence over surface water quality dynamics. High, positive discharge during the wet season yielded high dissolved organic carbon concentrations while low net discharge during the transitional and dry seasons was more correlated with high inorganic nutrient concentrations. Benthic flux data from batch core experiments showed consistent sediment uptake of nitrate/nitrite and phosphate and release of ammonium to the water column. Phosphate addition resulted in increased P uptake from water column. Understanding the seasonal dynamics in materials exchange at these local scales combined with fluxes at the landscape level (e.g., upstream vs. downstream) will allow us to better understand the role of mangrove ecotone in governing the net exchange of materials between the Everglades and Florida Bay.