Urban groundwater development was traditionally constrained by concerns about its quality. This study was conducted in the regions of La Ribera Alta and Ribera Baja and La Plana de Requena-Utiel of the Valencian Community (Valencia, Spain) where population density, demand for drinking water and agricultural activities are high. Groundwater bodies (GWBs) are regarded as management areas within each territory, and were used to establish protection policies. This study analyzed eleven GWBs. We used two databases with microbiological measurements from 154 wells over a 7-year period (2004-2011), risk factors and groundwater information. Wells were grouped according to frequency of microbiological contamination using E. coli measurements, category <1, or wells with low-frequency microbiological contamination and high-frequency wells or category 1-100, according to World Health Organization (WHO) quality criteria of drinking water. Of all wells, 18.12% showed high-frequency microbiological contamination with a majority distribution in the Ribera Alta region (26.98%, p < 0.001). No significant differences were found between the two risk categories for flow, static level, well depth and distance from population centres. This paper reveals that the vulnerability classes established by the Geological and Mining Institute of Spain (IGME) do not match the microbiological results, and that only eight wells with high-frequency contamination coincide with the high vulnerability areas.