Superparamagnetic Iron Oxide Nanoparticles (SPIONs) are used extensively in multiple biomedical applications such as hyperthermia, MRI enhancing reagents and drug delivery. However, despite their wide spread application, their environmental impacts, especially on the aquatic environment are not well understood. Daphnia magna (water fleas) are keystone species ubiquitous in freshwater ecosystems and are one of the most common species used in toxicity testing. This research combines magnetic resonance imaging, relaxometry and metabolomics (both in-vivo and ex-vivo) to build a holistic understanding of SPION toxicity. SPIONs with three different core sizes (8 nm, 10 nm, 12 nm), and three different ligand sizes (1 KD, 5 KD, 10 KD) were exposed to Daphnia over 24h. The impacts and potential compartmentalization was firstly evaluated by T2 weighted MRI. Secondly, T1 and T2 weighted 2D NMR analyses provided complementary information on the types of biomolecules that interact with the SPIONs inside the organisms. Finally, 2D in-vivo metabolomics provides insight into how the organisms themselves respond on exposure which helps explain the toxic-mode-of-action of the nanoparticles. To our knowledge this is the first time MRI, relaxometry and metabolomics have been combined to provide a comprehensive overview of toxicity inside whole organisms.