This study presents a sodium alginate/chitosan/activated carbon (SA/CS/AC) gel microspheres loaded with citrus peel allelochemicals for continuous inhibition of Microcystis aeruginosa by controlled release. Preparation parameters were optimized via response surface methodology (RSM) for improved algal inhibition, yielding an optimal formulation: 1.97% SA, 0.76% CS, 0.31% AC. The optimized gel microspheres showed a 7-day inhibition rate of 85.17 ± 2.49%, consistent with the predicted 85.29%. Characterization revealed that AC enriched the gel’s porous structure and surface functionality, increasing allelochemical adsorption sites, enhancing loading efficiency, and sustaining long-term release with a 25-day cumulative release of 70%. Algal inhibition declined slightly from day 7 to 30 due to allelochemical depletion but remained 76.27%, versus 30.58% for the blank SA/CS/AC carrier and 52.81% for the allelochemical-loaded SA/CS gel microspheres. AC thus synergistically strengthens algal inhibition by elevating allelochemical loading and prolonging activity, providing a feasible strategy for sustainable cyanobacterial bloom control.