A magnetic solid phase extraction method based on agarose coated magnetic nanoparticles)ACMNPs(coupled to a new magnetic field agitation (MFA) device was developed and investigated for the separation, preconcentration and determination of Pd(II) in aqueous solutions. For the first time, the formation of the nanoparticles and their encapsulation in agarose micro-flakes was conducted in a single step. For this purpose, preparation of the magnetic iron oxide nanoparticles was performed in an alkaline agarose solution. The sizes of Fe3O4 nanoparticles and agarose micro-flakes were 10-14 nm and 90-130 μm, respectively. The nanomagnetic agarose particles were functionalized by iminodiacetic acid and subjected to magnetic field agitation in the MFA device. The influence of different analytical parameters such as pH, ionic strength, type and volume of desorption solvent and amount of the adsorbent on the preconcentration of Pd(II) were investigated. Eight replicated analysis at the optimized conditions, resulted in a recovery of 94.1% with an RSD of 5.2% for Pd(II). The detection limit of the method (3σ) was 47 ng L(-1) for the analyte. The method was successfully applied to the determination of Pd(II) in natural water samples.