The naturally occurring sodium alginate (SA) biopolymer from the Sargassum muticum (Yendo) Fensholt was employed as a green organocatalyst for the synthesis of 4H-pyran derivatives. The naturally extracted macromolecule was fully characterized using different analyses, including nuclear magnetic resonance (NMR), Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and Energy Dispersive X-ray Analysis (EDX). The catalytic activity of SA was investigated in the one-pot reaction between aldehydes, malononitrile, and 1,3-dicarbonyl compounds in water at room temperature, and the corresponding 2-amino-3-cyano-4H-pyran derivatives were obtained with good to excellent yields. This organocatalyst was easily separated from the reaction mixture and reused for at least two consecutive cycles without a significant loss of its catalytic activity or selectivity. From the mechanistic point of view, density functional theory (DFT) and NCI analyses were performed for the first time to explain the regioselectivity outcomes for the synthesis of 2-amino-3-cyano-4H-pyran derivatives using SA as a green organocatalyst.