Body size constrains prey–predator interactions and physiology, therefore plankton size spectra have been appointed as synthetic descriptors of plankton community structure and functioning. Recently developed imaging systems and supervised classification tools provide size measurements of any object in situ or in net samples and automatically classify them into previously defined categories. But because the nature of objects detected by these imaging systems is diverse, from non-living detritus to organisms of different plankton taxa, and because the steps in the analysis could introduce specific biases, a careful analysis of such plankton size spectra is needed before going deeper into ecological considerations. Using a WP2 net time series, we propose a general framework to analyze and validate zooplankton size spectra collected with nets and analyzed with the ZooScan integrated system that includes supervised classification. Size spectra were controlled, at each step of the procedure, to assess the modification of their shape due to several possible biases: (i) the effect of objects touching each other during the image acquisition, (ii) the error of the automatic classification differing among size classes and (iii) the choice of model to estimate body biovolume.