What the statewide pattern says
A carbonate-valley pattern
Pennsylvania's higher nitrate is concentrated in limestone farm valleys — Lancaster County above all — where intensive agriculture and fast groundwater pathways coincide.
Southeastern Pennsylvania is one of the most intensively farmed crop-and-livestock regions in the East. In the carbonate valleys, fractured limestone gives surface nitrogen fast pathways into groundwater. That combination — heavy nitrogen input plus vulnerable aquifer — is the recipe national USGS work associates with higher nitrate in shallow groundwater and drinking-water wells (Nolan and Hitt, 2006).
Pennsylvania's own groundwater studies make the pattern more specific. In the lower Susquehanna basin, wells in agricultural carbonate-bedrock areas exceeded 10 mg/L far more often than wells in other rock settings, and nitrate was strongly correlated with manure application rate (USGS WRI 97-4146). Statewide monitoring later found nitrate above the federal limit in only about 3% of samples, with the highest result in a heavily farmed limestone valley and the greatest vulnerability in the Ridge-and-Valley and Piedmont carbonate areas (USGS SIR 2021-5119).
The Great Valley carbonate work explains why these valleys behave differently. Nitrate there does not necessarily decline with depth, and movement through fractures and solution channels can be rapid and difficult to predict (USGS WRI 95-4099). In Lancaster County dolomite, recharge through fractures and sinkholes changed groundwater nitrate within days of manure application (Gerhart, 1986). Isotope work in the lower Susquehanna traced the nitrogen to manure and, in places, sewage rather than synthetic fertilizer alone (USGS WSP 2497).
The northern half of the state reads differently for a reason that is geological rather than agricultural: in north-central and northeastern Pennsylvania, reducing conditions in the aquifer strip nitrate out, so a low reading there is not evidence that nitrogen never arrived (Cravotta and others, 2021). This is the clearest case on the site of why low nitrate cannot be read as clean water.