Pollution is one of the main anthropogenic threats to marine ecosystems. Studies analysing the accumulation and transfer of contaminants in planktonic food webs tend to rely on samples collected in discrete water bodies. Here, we assessed the representativeness of measurements at the chlorophyll-a maximum layer during the MERITE-HIPPOCAMPE cruise for the entire water column by investigating the vertical distribution of particles and plankton obtained by in-situ optical profilers at nine stations across the Mediterranean Sea. We identified specific conditions where the interpretation of results from contaminant analyses can be improved by detailing plankton size structure and vertical distributions. First, the presence of higher than usual plankton concentrations can result in sampling issues that will affect biomass estimation within each size class and therefore bias our understanding of the contaminant dynamics. Secondly, the presence of an unsampled water layer with high zooplankton biomass might imply non-resolved contaminant pathways along the trophic structure. This study lays the basis for optimizing sampling strategy in contaminant studies.