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We quantified sediment-water interface and water column nitrogen (N) transformation rates seasonally over the course of a year that incorporated a major storm event and a period of prolonged riverine base flow in Copano Bay, Texas, a shallow, productive estuary in the western Gulf of Mexico. We calculated daily rates of gross primary production (GPP), community respiration (CR), and net ecosystem production (NEP) in Copano Bay to examine carbon (C) cycling over the course of the year. These metrics of estuarine ecosystem function indicated that the estuary switched from a net sink for N during floods to a net source of N during droughts while sustaining high rates of primary production throughout the year. The estuary became a net sink for N as a result of increased denitrification rates following a storm event. Both GPP and CR increased immediately following a flood event, and the system was driven to net heterotrophy. Copano Bay became a net source of N during periods of prolonged base flow via increased N fixation rates. Internal N cycling became increasingly important during periods of base flow, including increased rates of dissimilatory nitrate reduction to ammonium. This internal N cycling sustained production during periods of drought, when GPP < CR. Both CR and NEP were linked to nutrient export from the inflowing rivers. N and C cycles were tightly linked but became decoupled briefly as a result of inputs of nutrients and organic matter during the period after a major storm event.

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Ecosystem function measurements can enhance our understanding of nitrogen (N) delivery in coastal catchments across river and estuary ecosystems. Here, we contrast patterns of N cycling and export in two rivers, one heavily influenced by wastewater treatment plants (WWTP), in a coastal catchment of south Texas. We measured N export from both rivers to the estuary over 2 yr that encompass a severe drought, along with detailed mechanisms of N cycling in river, tidal river, and two estuary sites during prolonged drought. WWTP nutrient inputs stimulated uptake of N, but denitrification resulting in permanent N removal accounted for only a small proportion of total uptake. During drought periods, WWTP N was the primary source of exported N to the estuary, minimizing the influence of episodic storm‐derived nutrients from the WWTP‐influenced river to the estuary. In the site without WWTP influence, the river exported very little N during drought, so storm‐derived nutrient pulses were important for delivering N loads to the estuary. Overall, N is processed from river to estuary, but sustained WWTP‐N loads and periodic floods alter the timing of N delivery and N processing. Research that incorporates empirical measurements of N fluxes from river to estuary can inform management needs in the face of multiple anthropogenic stressors such as demand for freshwater and eutrophication.