Nitrogen flux into the coastal environment via submarine groundwater discharge may be modulated by microbial processes such as denitrification, but the spatial scales at which microbial communities act and vary are not well understood. In this study, we examined the denitrifying community within the beach aquifer at Huntington Beach, California, where high-nitrate groundwater is a persistent feature. Nitrite reductaseencoding gene fragments (nirK and nirS), responsible for the key step in the denitrification pathway, were PCR amplified, cloned, and sequenced from DNAs extracted from aquifer sediments collected along a cross-shore transect, where groundwater ranged in salinity from 8 to 34 practical salinity units and in nitrate concentration from 0.5 to 330 M. We found taxonomically rich and novel communities, with all nirK clones exhibiting <85% identity and nirS clones exhibiting <92% identity at the amino acid level to those of cultivated denitrifiers and other environmental clones in the database. Unique communities were found at each site, despite being located within 40 m of each other, suggesting that the spatial scale at which denitrifier diversity and community composition vary is small. Statistical analyses of nir sequences using the Monte Carlo-based program ͐-Libshuff confirmed that some populations were indeed distinct, although further sequencing would be required to fully characterize the highly diverse denitrifying communities at this site.Denitrification, the microbial dissimilatory reduction of nitrate and nitrite to gaseous products (NO, N 2 O, and N 2 ) under suboxic conditions, has long been considered the main biological loss term for fixed nitrogen from ecosystems. In coastal and estuarine sediments, this process can remove more than half of the inorganic nitrogen inputs from terrestrial systems (27). One source of nitrogen for coastal environments is submarine groundwater discharge from unconfined aquifers, which is increasingly recognized as an important source of nutrients (7,16). Groundwater below the beach face at Huntington Beach (HB), California, is enriched in nitrate, with reported nitrate concentrations in excess of 400 M (3). The source of this nitrate is unknown, but potential sources include infiltration of fertilizercontaminated surface water, microbial nitrification, or leaking subsurface sewage lines. Nitrate concentrations in the groundwater pool decrease 2 orders of magnitude in the cross-shore direction as the nitrate-rich brackish groundwater mixes with saline, nitrate-depleted seawater (Fig. 1). This mixing establishes ideal gradients in both nitrate and salinity over which to examine the geochemical parameters that may be controlling microbial diversity, especially the diversity of denitrifying bacteria.Because denitrifying microorganisms span a wide range of taxonomic groups, including over 50 different genera (32), 16S rRNA-based approaches are not generally useful for investigating natural denitrifying communities. Nitrite reduction to nitric oxide is the rate-limi...