Nanomaterials with mixed composition, in particular magnetic spinel ferrites, are emerging as efficient contrast agents for magnetic resonance imaging (MRI). Many factors, including size, composition, atomic structure, and surface properties are crucial in the design of such nanoparticle-based probes due to their influence on the magnetic properties. Silica-coated iron oxide (IO-SiO(2)) and cobalt ferrite (CoIO-SiO(2)) nanoparticles were synthesized using standard high temperature thermal decomposition and base-catalyzed water-in-oil microemulsion techniques. Under neutral aqueous conditions, it was found that 50-75% of the cobalt content in the CoIO-SiO(2) nanoparticles leached out of the core structure. Leaching caused a 7.2-fold increase in longitudinal relaxivity and an increase in the saturation magnetization from ~48 emu/g core to ~65 emu/g core. X-ray absorption fine structure studies confirmed that the atomic structure of the ferrite core was altered following leaching, while TEM and DLS confirmed that the morphology and size of the nanoparticle remained unchanged. The CoIO-SiO(2) nanoparticles converted from a partially inverted spinel cation arrangement (unleached state) to an inverse spinel arrangement (leached state). The control IO-SiO(2) nanoparticles remained stable with no change in structure and negligible changes in magnetic behavior. This detailed analysis highlights how important understanding the properties of nanomaterials is in the development of reliable agents for diagnostic and therapeutic applications.