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Nitrate in the groundwater of the lower Yakima Valley, Washington frequently exceeds the Environmental Protection Agency (EPA) maximum contaminant level standard for potable water (10 mg/L), impacting communities with disadvantaged socioeconomic status. Nitrogen and oxygen isotopic signatures were determined for nitrate in soil leachates and irrigation return flow. Isotope signatures for nitrate from soil leachate had significant overlap with both the isotope signatures of naturally occurring soil nitrate at the nearby Hanford site, Washington and of groundwater nitrate attributed to manure and fertilizer application in a local EPA study. A mass balance calculation using Delta O-17 data suggests that there is a consistent similar to 9% atmospheric contribution to nitrate in soil accumulations below caliche layers at several locations. This agrees with other research on the atmospheric contribution to naturally occurring soil nitrates in areas with similar mean annual precipitation values. We argue that this consistent similar to 9% atmospheric component indicates that soil nitrate at depth is dominated by naturally occurring, biologically fixed nitrate across multiple sites. We suggest the flushing of naturally occurring soil nitrate to groundwater during land use conversion to irrigated agriculture may represent a previously overlooked significant nitrate input to aquifers in this region.