Abstract. Interactions among geomorphology, circulation, and biogeochemical cycling determine estuary responses to external nutrient loading. In order to better manage watershed nutrient inputs, the goal of this study was to develop seasonal dissolved inorganic nitrogen (DIN) and phosphorus (DIP) budgets for the two estuaries in south Florida, the Caloosahatchee River estuary (CRE) and the St. Lucie Estuary (SLE), from 2002 to 2008. The Land-Ocean Interactions in the Coastal Zone (LOICZ) approach was used to generate water, salt, and DIN and DIP budgets. Results suggested that internal DIN production increases with increased DIN loading to the CRE in the wet season. There were hydrodynamic effects as water column concentrations and ecosystem nutrient processing stabilized in both estuaries as flushing time increased to > 10 d. The CRE demonstrated heterotrophy (net ecosystem metabolism or NEM < 0.0) across all wet and dry season budgets. While the SLE was sensitive to DIN loading, system autotrophy (NEM > 0.0) increased significantly with external DIP loading. This included DIP consumption and a bloom of a cyanobacterium (Microcystis aeruginosa) following hurricane-induced discharge to the SLE in 2005. Additionally, while denitrification provided a microbiallymediated N loss pathway for the CRE, this potential was not evident for the SLE where N 2 fixation was favored. Disparities between total and inorganic loading ratios suggested that the role of dissolved organic nitrogen (DON) should be assessed for both estuaries. Nutrient budgets indicated that net internal production or consumption of DIN and DIP fluctuated with inter-and intra-annual variations in freshwater inflow, hydrodynamic flushing, and primary production. The results of this study should be included in watershed management plans in order to maintain favorable conditions of external loading relative to internal material cycling in both dry and wet seasons.