What the statewide pattern says
A Snake River Plain pattern
Idaho's higher nitrate tracks the Snake River Plain aquifer system: shallow, irrigation-recharged sediments and fractured basalt under some of the heaviest dairy and irrigated-crop country in the West.
The Treasure Valley — Canyon County and its neighbors — leads the public-system map, and it sits in a setting the state already watches: Idaho DEQ's nitrate priority areas include northeast Canyon County, where septic density adds to the agricultural signal over shallow aquifers. The Idaho Geological Survey is currently modeling septic nitrate loading there to guide development rules (Idaho DEQ and Idaho Geological Survey programs).
Downstream, the Magic Valley is the dairy heartland, and its shallow fringe runs hot. The eastern Snake River Plain aquifer is famously productive, but where it thins and pinches out toward the Snake River, shallow groundwater dominates: USGS modeling links that geometry to the valley's elevated nitrate (Rupert and others, 2014). Idaho DEQ's worst-ranked nitrate priority area, Marsh Creek, averaged 6.8 mg/L with a maximum of 40 mg/L in the 2020 assessment, and regional trend work finds nitrate still rising in parts of the mid-Snake (Skinner, 2022).
The supported source reading is agricultural — manure-heavy in the Magic Valley dairy country, fertilizer-and-septic in the Treasure Valley — not a certified source at any individual system. Regionally the basalt aquifer keeps most of its deep water low — about 3 percent of Snake River Plain wells exceeded the limit in USGS's assessment — so the pattern is a shallow-fringe problem more than a whole-aquifer one (Nolan and Hitt, 2006).