Daphnia magna is a freshwater crustacean and model organism for toxicology. Daphnia magna were fed with TiO2 anatase nanoparticles, fixed, embedded and sectioned according to routine electron microscopy protocols and correlatively investigated by secondary electrons (SE), scanning transmission helium ion microscopy (STHIM) and secondary ion mass spectrometry (SIMS). Since SE imaging gives information about the sample surface, no information of biological tissue can be retrieved from flat sections, but TiO2 anatase nanoparticles localized in the gut of the animal can still be visualized due to their intrinsic structure. Using STHIM, biological structures of the gut epithelial cells, such as Villi (V), cell borders (arrows) and the basal labyrinth (bas lab) can be readily identified (top row). STHIM therefore facilitates recognition and orientation of biological structures in flat sections that are inaccessible to SE imaging. The middle row shows correlative high resolution SE and SIMS imaging of the TiO2 nanoparticles – epithelium interface: While SE imaging just reveals the TiO2 nanoparticles, SIMS allows the detection of CN- cluster-ions (as a marker for biological tissue) and the detection of jTi+ + kTiO+ ions (i.e. all isotopes of Ti+ and TiO+ in order to increase dynamic). The obtained chemical maps can be superimposed, and false colour coded to identify co-localizations of secondary ion-species, allowing the precise localization of nanoparticles in biological tissues. The bottom row shows mass spectra obtained in positive and negative SIMS mode from the region of interest presented in the middle row, highlighting the benefit of the focal plane detector, as a multitude of secondary ions can be investigated at the same time in a chosen mass range.