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Anthropogenic nitrogen (N) pollution has increased dramatically over recent decades, causing detrimental effects on coastal marine environments, where primary production is often limited by N. River networks are important linkages between watersheds and estuaries, and are also sites for N processing. At the interface between rivers and estuaries, tidal freshwater zones (TFZs) emerge. Because of tidal energy, flow slows down or can even reverse direction in TFZs, resulting in prolonged water residence times. Long water residence times make TFZs potential N cycling “hotspots”, modifying N fluxes immediately upstream of estuaries. However, N transport and transformations within TFZs have not been studied widely. This dissertation work explored spatial and temporal variations of N and phytoplankton in the TFZs of two south Texas rivers (the Mission and Aransas rivers). The results suggest that, on an annual basis, TFZs can be important sinks for total N under baseflow conditions. Along the TFZs, spatial gradients of N emerged downstream of major N inputs, where dissolved inorganic N (DIN) was transformed into organic forms, primarily through phytoplankton uptake. An in-depth analysis of the Aransas River system revealed temperature and nutrients as the primary controls of phytoplankton biomass and community composition. In winter, high nutrients (particularly DIN) supported high phytoplankton biomass, dominated by cryptophytes and diatoms. In summer, low-nutrient water supported lower biomass, and the community was dominated by cyanobacteria. Modeling of N transport and biogeochemical processing within the Aransas River provided additional insights about linkages between water residence times and processing effects at different locations – daily DIN uptake rates were highest at the upper Aransas River TFZ, but cumulative DIN uptake was much greater at the lower TFZ due to longer water residence time. As modeled DIN inputs increased, however, the capacity of the TFZ to retain N was challenged. The upper TFZ reached N saturation faster than the lower TFZ, and complete saturation of DIN for the whole system occurred with N inputs between 8 and 16 times the current levels. These elevated levels were equivalent to DIN discharged from a medium-sized city in this watershed, with a population of 300,000 – 640,000. This dissertation highlighted the role that TFZs play in retaining watershed-derived N at the river/estuary interface and provided insights on management of coastal eutrophication