Archeological sites close to coastal volcanic-sedimentary aquifers are threatened by groundwater contaminated by natural and anthropogenic processes. The paper reports on a hydrogeological, chemical (major, minor and trace elements) and isotopic (δD-H2O, δ18O-H2O, δ15N-NO3, δ18O-NO3, δ11B, 222Rn) survey of groundwater at the Cumae archaeological site, which is located in the coastal north-western sector of the volcanic district of Phlegraean Fields (southern Italy), where groundwater flooding phenomena occur. Results show the presence of a complex coastal volcanic-sedimentary aquifer system where groundwater quality is influenced mainly by: (i) aquifer lithology and localized ascent of magmatic fluids along buried volcano-tectonic discontinuities, (ii) mixing of groundwater, deep mineralized fluids and seawater during groundwater pumping, and (iii) nitrate contamination >50 mg/L from non-point agricultural sources. Moreover, δD and δ18O point toward fast recharge from seasonal precipitations, while the isotopic ratios of N and O in nitrate reveal the contribution of mineral and organic fertilizers as well as leakage from septic tanks. Results can assist the local archaeological authority for the safeguarding and management of the archaeological heritage of the Cumae site.