A few number of soil profile studies have pointed out that Joso Clay, a thick clayey layer underlying the shallow groundwater bodies in the diluvial uplands of southern Ibaraki and northern Chiba prefectures, Japan, has a structured surface layer in which the hydraulic conductivity is one to several orders of magnitude higher than that of the underlying massive layer. The spatial distribution of the boundary between the structured and massive clay layers should be determined as the aquifer–aquitard boundary; however, such attempts have not been made. In the present study, dynamic cone penetrometry was used to determine the spatial distribution of the aquifer–aquitard boundary in Joso Clay at a field scale in Tsukuba–Inashiki Upland, Ibaraki prefecture, Japan. The dynamic cone penetration index Nd5, every 5-cm depth average of the number of hammer strikes required for the tip cone to enter into the soil per unit of depth, was determined to a depth of 3.1–3.7 m at 54 rectangular grid points with approximately 5-m spacing in a field with an area of 943 m2. The field-scale Nd5 profile data suggested that prismatic structures with Nd5 values of up to 50–60 m−1 are widely distributed in the uppermost layer of the Joso Clay. Accordingly, a criterion of Nd5 > 60 m−1 was proposed for determining the underlying aquitard in this field. The depth to the aquifer–aquitard boundary was determined to be 2.58 m on average, ranging from 2.40 to 2.89 m. Furthermore, annual water table monitoring at each grid point showed that the thickness of the structured layer, varying from 0.30 to 0.75 m, occupied 61–100% of the annual average shallow aquifer thickness, which varied from 0.40 to 0.87 m. These results demonstrate the significance of the uppermost structured layer in the Joso Clay as the major part of the shallow aquifer at a field scale in this upland.