Natural compounds extracted from lichens represent a promising ecological alternative for controlling algal and cyanobacterial blooms in aquatic ecosystems. This study examines the anticyanobacterial and antimicroalgal potential of two volatile fractions (HE1 and HE2) extracted from the lichen Pseudevernia furfuracea (L.) Zopf., harvested from two Moroccan biotopes. Furthermore, the potential anticyanobacterial and antimicroalgal response mechanisms were investigated by analyzing the activity of antioxidant enzymes in the cyanobacterial species Microcystis aeruginosa and the green microalga Chlorella sorokiniana cells. In addition, a molecular docking analysis was performed to predict the experimental results, providing a mechanistic understanding of the main interactions of the identified compounds with cyanobacterial and microalgal targets. The results showed that both fractions (HE1 and HE2) inhibited the growth of M. aeruginosa and C. sorokiniana, with inhibition zone diameters of 12.6–13.7 and 20.7–20.9 mm, respectively. Minimum inhibitory concentrations (MICs) ranged from 375 to 750 µg/mL. In liquid culture, both HE1 and HE2 fractions reduced cell density by more than 98% after 8 days of exposure and decreased chlorophyll-a and protein levels by more than 80% compared to the controls. Furthermore, HE1 and HE2 induced distinct oxidative responses: M. aeruginosa exhibited early and significant increases in superoxide dismutase (SOD) and catalase (CAT) activities, as well as high malondialdehyde (MDA) levels, while C. sorokiniana showed slower and more moderate activation, indicating greater resistance to oxidative stress. Molecular docking analysis (-3.9 to -8.4 kcal mol⁻¹) identified abietatriene, δ-cadinene, guaiac acetate, atraric acid, and chloroatranol as the main bioactive compounds in the two volatile fractions (HE1 and HE2) extracted from the lichen P. furfuracea. In conclusion, the volatile extracts of P. furfuracea exert potent and species-specific inhibitory effects on cyanobacteria and microalgae through oxidative and metabolic interferences, confirming their potential as ecofriendly agents to limit cyanobacterial and algal proliferation.