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Abstract The seasonal controls of hydrology, temperature, hypoxia, and biogeochemical conditions for groundwater ammonium–N (NH₄⁺) concentrations are not well understood. Here we investigated these controls for riparian groundwaters located upstream of two milldams over a period of 4 years. Groundwater chemistry was sampled monthly while groundwater elevations, hydraulic gradients, and temperatures were recorded sub‐hourly. Distinct seasonal patterns for NH₄⁺were observed which differed among the wells. For wells that displayed a strong seasonal pattern, NH₄⁺concentrations increased through the summer and peaked in October–November. These elevated concentrations were attributed to ammonification, suppression of nitrification, and/or dissimilatory nitrate reduction to ammonium (DNRA). These processes were driven by high groundwater temperatures, low hydraulic gradients (or long residence times), hypoxic/anoxic groundwater conditions, and increased availability of dissolved organic carbon as an electron donor. In contrast, NH₄⁺concentrations decreased in the riparian groundwater from January to April during cool and wet conditions. A groundwater well with elevated total dissolved iron (TdFe) concentrations had elevated NH₄⁺concentrations but displayed a muted seasonal response. In addition to hydrologic controls, we attributed this response to additional NH₄⁺contribution from Fe‐driven autotrophic DNRA and/or ammonification linked to dissimilatory Fe reduction. Understanding the temporal patterns and factors controlling NH₄⁺in riparian groundwaters is important for making appropriate watershed management decisions and implementing appropriate best management practices. 

Abstract Groundwater nitrate‐N isotopes (δ¹⁵N‐) have been used to infer the effects of natural and anthropogenic change on N cycle processes in the environment. Here we report unexpected changes in groundwater δ¹⁵N‐ for riparian zones affected by relict milldams and road salt salinization. Contrary to natural, undammed conditions, groundwater δ¹⁵N‐ values declined from the upland edge through the riparian zone and were lowest near the stream. Groundwater δ¹⁵N‐ values increased for low electron donor (dissolved organic carbon) to acceptor ratios but decreased beyond a change point in ratios. Groundwater δ¹⁵N‐ values were particularly low for the riparian milldam site subjected to road‐salt salinization. We attributed these N isotopic trends to suppression of denitrification, occurrence of dissimilatory nitrate reduction to ammonium (DNRA), and/or effects of road salt salinization. Groundwater δ¹⁵N‐ can provide valuable insights into process mechanisms and can serve as “imprints” of anthropogenic activities and legacies. 

Introduction Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function. Methods Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States. Results We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes ( amo A for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes ( nos Z) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification. Discussion Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.