Abstract The three-dimensional groundwater flow and the hydrogeochemical regime have been determined in the Bere Stream valley, North Dorset Downs, southern England. The dual porosity characteristics of the Portsdown Chalk have been established using geophysical and hydrochemical borehole logging. Chemical properties have been established using major and trace element analyses of depth samples and groundwaters. The study site is located at the unconfined-confined boundary of the Chalk aquifer, where it is overflowing in the observation boreholes. The Chalk dips locally at about 5 m/km to the south–east under Palaeogene confining beds and three distinctive flow horizons may be recognised. The Chalk groundwater is of Ca–HCO 3 type and three separate geochemical groundwater zones were also determined with depth, having different oxygen levels and trace element characteristics. (1) A shallow O 2-rich zone with around 80% dissolved O 2 and low trace element concentrations. (2) A mixing and transition zone with significant concentrations of trace elements and high trace metal concentrations at its base: manganese 29 μg/l, nickel 55 μg/l, cadmium 146 μg/l, and zinc 214 μg/l. (3) A deeper zone with depleted oxygen (5–20% dissolved O 2) and with longer water residence times shown by higher Mg/Ca and K/Na ratios as well as higher Sr and F. The groundwater geochemistry in the Chalk aquifer is dominated by incongruent reactions with the fine-grained carbonate sediments, which release trace element impurities to the water. Some of the metals are co-precipitated with Mn- and Fe-oxide phases on fissure surfaces, whilst producing a purer calcite. During subsequent recrystallisation to purer iron- and manganese-oxides on fissure surfaces under specific geochemical and hydrodynamic conditions, trace metals are released into the fissure water. The results demonstrate the need to monitor quality stratification and the changes in the groundwater baseline chemistry in areas close to the redox boundary which, in the dual porosity Chalk is likely to be a diffuse zone with exchange between oxygen poor matrix waters and more oxic water flowing through the fissures.