Resolving nitrogen dynamics across the river–estuary continuum requires observations that capture short-term variability and interfacial processes often missed by conventional monitoring. Here, we present results from a deployment of a high-frequency in situ sensor measuring nitrate + nitrite (NO₃⁻ + NO₂⁻) and nitrite (NO₂⁻) in a shallow, river-influenced estuary in Denmark. Our observations reveal clear daily variability in NO₃⁻ + NO₂⁻and NO₂⁻ concentrations which are linked to interactions between riverine inputs, sediment–water exchange, and biological activity. Our results highlight how sampling design influences data representativeness and demonstrate the value of high-frequency measurements improving our understanding of nitrogen cycling across the river–estuary continuum.