Horseradish peroxidase (HRP) characteristics were improved by two techniques, Na-alginate entrapment and glutaraldehyde crosslinking prior to alginate entrapment, in order to enhance the stability, functionality and removal of dyes in waste water. Free, entrapped and crosslinked-entrapped enzymes were compared by activity assays, which indicated the optimum temperature is 25 °C and pH 4.0-5.0. Kinetics results showed that alginate entrapment and crosslinking prior to entrapment increased Vmax and did not cause any significant decrease in Km. The thermal resistance of the free enzyme was short-term, zero residual activity after 250 min, while the immobilized enzymes preserved more than 50% of their activity for 5 h at 60 °C. Immobilized HRP was resistant to methanol, ethanol, DMSO and THF. The storage stability of free HRP ended in 35 days whereas entrapped and crosslinked-entrapped HRPs had 87 and 92% residual activity at the 60th day, respectively. HRP was used in the decolorization of azo dye Acid yellow 11 and total decolorization (>99%) was obtained using crosslinked-entrapped HRP. Reusability studies presented the improvement that crosslinked-entrapped HRP reached 74% decolorization after 10 batches. The results demonstrated that the novel immobilized HRP can be used as an effective catalyst for dye degradation of industrial waste effluents.