In this study we explored the cultivable fungal diversity in Lake Magadi and their secondary metabolite production. Isolation was done on alkaline media (Potato dextrose agar, Malt extract agar, Oatmeal agar and Sabouraud dextrose agar). A total of 52 unique isolates were recovered from the lake and were characterized using different techniques. Growth was observed at pH, temperature and salinity ranges of between 6 - 10, 25 °C - 40 °C and 0%–20% respectively. Phylogenetically, the isolates were affiliated to 18 different genera with Aspergillus, Penicillium, Cladosporium, Phoma and Acremonium being dominant. A screen for the ability to produce extracellular enzymes showed that different isolates could produce proteases, chitinases, cellulases, amylases, pectinases and lipases. Production of antimicrobial metabolites was noted for isolate 11M affiliated to Penicillium chrysogenum (99%). Cell free extracts and crude extracts from this isolate had inhibitory effects on Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, Salmonella spp., Shigella spp., Candida albicans and fungal plant pathogens Schizophyllum commune, Epicoccum sorghinum strain JME-11, Aspergillus fumigatus strain EG11-4, Cladosporium halotolerans CBS 119416, Phoma destructive and Didymella glomerata). In this study we showed that different cultivation strategies can lead to recovery of more phylotypes from the extreme environments. Growth under different physiological characteristics typical of the soda lake environment (elevated temperature, pH and salts) confirmed the haloalkaliphilic nature of the fungal isolates. The use of suitable antimicrobial production media can also lead to discovery of more phylotypes producing diverse biocatalysts and bioactive metabolites.