Abstract Through regular sampling surveys, the Flanders Marine Institute (VLIZ) is generating a long‐term data series for the Belgian coastal water and sandbank system, a designated site in the Long Term Ecological Research (LTER) network. The data series is built from sampling activities initiated in 2012 in the framework of the LifeWatch marine observatory. Nine nearshore stations are sampled monthly, with an additional eight offshore stations sampled seasonally. This paper presents the generated data series for zooplankton densities and size measurements, analysed using a ZooScan plankton imaging device together with the ZooProcess and Plankton Identifier software packages. To date 673.017 biological particles have been collected and identified. The collection and processing of the 2012–2018 dataset is described, along with its data curation and quality control. Yearly versions of the data are published in a standardized format together with environmental parameters, accompanied by an extensive metadata description and labelled with digital identifiers for traceability. The data are published under a CC‐BY 4.0 license, allowing use of the data under the condition of providing the reference to the original source.