Spatially heterogeneous and temporally variable nutrient concentrations (P, N) in near‐surface aquifers are common and are driven by different factors such as climate, topography, vegetation, sediment compositions, and water level fluctuations. Nonetheless, the identification of discrete areas where similar concentrations patterns can be expected is still difficult, especially in patchy systems such as riparian zones of lowland rivers. To address this challenge, a floodplain aquifer of the river Spree (Germany) has been investigated by sampling groundwater with high vertical and horizontal resolutions. Vertical nutrient distributions measured by multi‐level samplers with a 10 cm resolution indicate a biogeochemical layering of the aquifer. High concentrations in the upper 2 m can be attributed to a local redox gradient, which is induced by water level fluctuations and biological turnover processes, while the layer below is mainly influenced by medium‐scale to large‐scale groundwater flow patterns. High concentration in the upper part of the aquifer enforces groundwater sampling with a high horizontal resolution of 3 m from the near‐surface groundwater. The results compared with highly resolved elevation and sediment data indicate that geomorphological features and water level fluctuations control the thickness of the unsaturated zone and the redox gradient. The strength of the gradient and the amount of degradable organic matter determine the intensity of nutrient release by chemical reactions and biological turnover. Copyright © 2014 John Wiley & Sons, Ltd.