Microalgae and cyanobacteria are rich sources of numerous phytochemical compounds with intrinsic antifungal potential. This research aimed to screen the phytochemical compounds and contents, as well as the antioxidant profiles, in eight cyanobacterial and two microalgal strains isolated from soil and brackish water habitats in Egypt. Our study also evaluated their antifungal activities against three phytopathogenic fungi—namely, Pythium ultimum, Fusarium solani, and Botryodiplodia theobromae, which are known to cause severe plant loss. The biochemical compounds were obtained from the cyanobacterial and algal methanolic extracts, and were identified through comparative phytochemical analyses related to the inhibition of the fungal pathogens. Comparative qualitative analyses of alkaloids, steroids, glycosides, and saponins were also carried out. The quantitative phytochemical screening of the cyanobacterial and algal strains investigated revealed the presence of xylanase, glucanase, and chitinase enzymes, along with some bioactive compounds, such as phenolics, flavonoids, proteins, neutral sugars, and carotenoids, which were species-dependent and detected in variable amounts in the extracts. The unicellular green microalgal strain Dunaliella sp. HSSASE13 displayed the highest level of antioxidant activity. However, the highest antifungal activities were shown by the heterocystous cyanobacterial strain Anabaena sp. HSSASE11 (83.94%), followed by Dunaliella sp. HSSASE13 (81.94%) and the non-heterocystous cyanobacterial strain Oscillatoria nigro-viridis HSSASE 15 (63.42%), against the three fungal pathogens B. theobromae, F. solani, and P. ultimum, respectively. Our results indicate that the highest significant and positive correlations of flavonoids (r = 0.854), phenolics (r = 0.785), DPPH scavenging activity (r = 0.876), total proteins (r = 0.808), xylanase activity (r = 0.876), glucanase activity (r = 0.746), and total neutral sugars (r = 0.764), in terms of their antifungal activities, were recorded against F. solani. Conclusively, the cyanobacterial and algal strains tested in the present study can be useful agents for the management and biocontrol of plant-infecting fungal pathogens.