Marine algae are a valuable source of polysaccharides. However, the information available on sulfated polysaccharides from microalgae is limited. Navicula sp. is a microalga present in the Sea of Cortez, of which little is known regarding their polysaccharides’ properties. This study investigated the physicochemical and microstructural characteristics of Navicula sp. sulfated polysaccharide (NSP). The Fourier transform infrared spectrum of NSP showed distinctive bands (1225 and 820 cm−1, assigned to S–O and C–O–S stretching, respectively), confirming the molecular identity. NSP registered molecular weight, intrinsic viscosity, a radius of gyration, and a hydrodynamic radius of 1650 kDa, 197 mL/g, 61 nm, and 36 nm, respectively. The zeta potential, electrophoretic mobility, conductivity, and diffusion coefficient of the molecule were −5.8 mV, −0.45 µm cm/s V, 0.70 mS/cm, and 2.9 × 10−9 cm2/s, respectively. The characteristic ratio and persistence length calculated for NSP were 4.2 and 1.3 nm, suggesting a nonstiff polysaccharide chain conformation. The Mark–Houwink–Sakurada α and K constants were 0.5 and 1.67 × 10−1, respectively, indicating a molecular random coil structure. NSP scanning electron microscopy revealed a rough and porous surface. Knowing these polysaccharides’ physicochemical and microstructural characteristics can be the starting point for elucidating their structure–function relationship as a valuable tool in advanced biomaterial design.