The increasing use of biofunctionalized magnetic nanoparticles in biomedical applications calls for further development of characterization tools that allow for determining the interactions of the nanoparticles with the biological medium in situ. In cell-incubating conditions, for example, nanoparticles may aggregate and serum proteins adsorb on the particles, altering the nanoparticles' performance and their interaction with cell membranes. In this work we show that the aggregation of spherical magnetite nanoparticles can be detected with high sensitivity in dense, highly light scattering media by making use of magnetically induced birefringence. Moreover, the hydrodynamic particle diameter distribution of anisometric nanoparticle aggregates can be determined directly in these media by monitoring the relaxation time of the magnetically induced birefringence. As a proof of concept, we performed measurements on nanoparticles included in an agarose gel, which scatters light in a similar way as a more complex biological medium but where particle-matrix interactions are weak. Magnetite nanoparticles were separated by agarose gel electrophoresis and the hydrodynamic diameter distribution was determined in situ. For the different particle functionalizations and agarose concentrations tested, we could show that gel electrophoresis did not yield a complete separation of monomers and small aggregates, and that the electrophoretic mobility of the aggregates decreased linearly with the hydrodynamic diameter. Furthermore, the rotational particle diffusion was not clearly affected by nanoparticle-gel interactions. The possibility to detect nanoparticle aggregates and their hydrodynamic diameters in complex scattering media like cell tissue makes transient magnetic birefringence an interesting technique for biological applications.