Biocompatible magnetic hydrogels provide a great source of synthetic materials, which facilitate remote stimuli, enabling safer biological and environmental applications. Prominently, the ex situ and in situ magnetic phase integration are used to fabricate magneto-driven hydrogels, exhibiting varied behaviours in aqueous media. Therefore, it is essential to understand their physicochemical properties to target the best material for each application. In this investigation, three different types of magnetic alginate beads were synthesised. First, by direct, ex situ, calcium chloride gelation of a mixture of Fe3O4 nanoparticles with an alginate solution. Second, by in situ synthesis of Fe3O4 nanoparticles inside of the alginate beads and third, by adding an extra protection alginate layer on the in situ synthesised Fe3O4 nanoparticles alginate beads. The three types of magnetic beads were chemically and magnetically characterised. It was found that, they exhibited particular stability to different pH and ionic strength conditions in aqueous solution. These are essential properties to be controlled when used for magneto-driven applications such as targeted drug delivery and water purification. Therefore, this fundamental study will direct the path to the selection of the best magnetic bead synthesis protocol according to the defined magneto-driven application.