Watershed-derived nitrogen (N) inputs from coastal watersheds can have a significant impact on estuarine function, with land use and stream network characteristics altering the timing, quantity and quality (labile vs. refractory) of this source. Excess N in estuarine ecosystems has led to increased rates of primary production (eutrophication), reduced biodiversity, habitat degradation and food web alterations. Nitrogen retention is particularly high in shallow headwater streams due to high biological activity, increased sediment surface to streamwater volume ratios and the fact that low order streams encompass a large proportion of total stream length within the stream network. Denitrification is one component of instream N retention that is particularly important because it removes N from the aquatic ecosystem. Two coastal plain watersheds of contrasting land uses (agricultural and silvicultural) located adjacent to the Neuse River Estuary were studied to assess the effect of hydrology on nutrient export, the factors controlling rates of denitrification in streambed sediments and the contribution of denitrification to instream N removal. Nitrate export was greatly affected by hydrodynamic conditions, with nutrient pulses observed during storm events, often increasing instream concentrations by 1-2 orders of magnitude. Factors that controlled denitrification varied by land use. Nitrate, organic carbon and elevated temperature stimulated rates in agricultural streams, but had minimal impact in silvicultural streams.

Instream nutrient retention determined by mass balance calculations showed the stream to be a significant sink for ammonium (46%) and phosphate (14%), but not nitrate. High rates of denitrification observed in the agricultural sediments following nitrate additions showed significant potential for denitrification, which responded linearly to increasing nitrate concentrations. However, the ability of denitrification to attenuate storm pulses of nitrate depends largely on hydrological transport of nitrate-rich streamwater to denitrifying communities in streambed sediments. Management of these drainage networks, including channel modifications to increase hyporheic flow (i.e. addition of woody debris or other channel obstructions) or to increase retention time (i.e. flashboard risers or streamside wetlands) may help reduce downstream export in streams that support high rates of denitrification.