Diffuse agricultural pollution is one of the greatest challenges to achieving good chemical and ecological status of Scotland’s water bodies. The River Ythan in Aberdeenshire was designated a Nitrate Vulnerable Zone (NVZ) in the year 2000, due to the eutrophication of the Ythan Estuary and rising nitrate trends in Private Water Supply (PWS) groundwater abstractions. The third River Basin Management Plan (RBMP) for Scotland reported the Ellon groundwater body of the River Ythan catchment to be of poor chemical status as of 2021 with respect to nitrate, and forecasted groundwater recovery beyond 2027. Following two decades of NVZ designation, we investigated the drivers of groundwater nitrate across the River Ythan catchment through an analysis of long-term (2009–2018) groundwater quality monitoring data collected by the Scottish Environmental Protection Agency (SEPA) and a recent synoptic groundwater nitrate sampling survey of PWSs. Groundwater nitrate was found to remain elevated across the catchment area, and appeared to be highly sensitive to agricultural practices and meteorological forcing, indicating a high sensitivity of groundwater quality to environmental change. Further hydrogeological characterisation is recommended to better understand the effects of agricultural practices on groundwater quality, and to facilitate achievement of future RBMP goals under a changing climate.