Careful extraction and analysis of porewater from sediment cores are critical for the investigation of small-scale biogeochemical processes. Firstly, small sample volumes and high spatial resolution are required. Secondly, several chemical species in the anaerobic porewater are sensitive to oxidation when brought in contact with ambient air. Here we present the combination of a special sampling technique and an analytical method for the porewater extraction of a varved sediment core from Lake Baldegg in central Switzerland, using MicroRhizon samplers and a portable capillary electrophoresis (CE) instrument. MicroRhizon filter tubes of 1 mm diameter and 20 mm length are suitable for fast retrieval of particle-free porewater samples directly from the sediment core. Since the time-span between sampling and analysis is less than 20 seconds, oxygen-sensitive Fe(ii) can be analyzed in one go together with Na(+), K(+), Ca(2+), Mg(2+), NH4(+), and Mn(ii) without splitting, acidification or dilution of the sample. The major inorganic cations and anions of the sediment porewater can be determined in less than 15 minutes. Detection limits are in the sub-micromolar concentration range. The capillary electrophoresis instrument used in this study requires sample volumes of only 20 μL. These remarkable small sample volumes allow the minimization of disturbance of the sediment cores and a high spatial resolution of the sediment profile, even in sediments with low water content. The equipment is inexpensive, easy to handle, fully portable and therefore suitable for environmental on-site applications.