Recently, the subsoils of ephemeral stream (arroyos) floodplains in the northern Chihuahuan Desert were discovered to contain large naturally occurring NO₃⁻ reservoirs (floodplain: ~38,000 kg NO₃-N/ha; background: ~60 kg NO₃-N/ha). These reservoirs may be mobilized through land use change or natural stream channel migration which makes differentiating between anthropogenic and natural groundwater NO₃⁻ sources challenging. In this study, the fate and sources of NO₃⁻ were investigated in an area with multiple NO₃⁻ sources such as accidental sewer line releases and sewage lagoons as well as natural reservoirs of subsoil NO₃⁻. To differentiate sources, this study used a large suite of geochemical tools including δ¹⁵N[NO₃], δ¹⁸O[NO₃], δ¹⁵N[N₂], δ¹³C[DIC], ¹⁴C, tritium (³H), dissolved gas concentrations, major ion chemistry, and contaminants of emerging concern (CEC) including artificial sweeteners. NO₃⁻ at sites with the highest concentrations (25 to 229 mg/L NO₃-N) were determined to be largely sourced from naturally occurring subsoil NO₃⁻ based on δ¹⁵N[NO₃] (<8 ‰) and mass ratios of Cl⁻/Br⁻ (〈100) and NO₃⁻/Cl⁻ (>1.5). Anthropogenic NO₃⁻ was deciphered using mass ratios of Cl⁻/Br⁻ (>120) and NO₃⁻/Cl⁻ (<1), δ¹⁵N[NO₃] (>8 ‰), and CEC detections. Nitrogen isotope analyses indicated that denitrification is fairly limited in the field area. CEC were detected at 67 % of sites including ³H dead sites (<1 pCi/L) with low percent modern carbon-14 (PMC; <30 %). Local supply wells are ³H dead with low PMC; as ³H does not re-equilibrate and ¹⁴C is very slow to re-equilibrate during recirculation through infrastructure, sites with low PMC, ³H < 1 pCi/L, and CEC detections were interpreted as locations with substantial anthropogenic groundwater recharge. Neotame was used to identify locations of very recent (<15 years before present) or ongoing wastewater influxes to the aquifer. This work shows the important influence of naturally occurring subsoil NO₃⁻ reservoirs on groundwater in arid regions and the major contribution of artificial recharge.