Aim: Fungi that can tolerate unfavorable conditions are a potential source of stable bioactive metabolites that can be used for various industrial processes. Therefore this study aimed to isolate halotolerant and halophilic fungi from the Iko river estuary and screen them for three industrially important enzymes: amylase, cellulase, and mannanase. Place and Duration of Study: Department of Microbiology, Akwa Ibom State University, Nigeria, between September 2021 and August 2022. Methodology: Five sediment-dwelling fungi isolated from three locations along the Iko river estuary were assayed for their halotolerance on PDA containing different NaCl concentrations while their amylolytic, cellulolytic, and mannolytic activities were evaluated on agar plates containing 10% NaCl. The highest producer of the screened enzymes was identified using molecular techniques and further subjected to various submerged fermentation conditions to optimize the production of salt tolerant amylase, cellulase, and mannanase. Results: All isolates were halotolerant, best adapted to a salinity of 5% NaCl (w/v), and capable of secreting at least one of the three tested enzymes in 10% NaCl (w/v). Aspergillus niger isolate L2S1 had the highest enzymatic index among other isolates thus requiring optimization. The optimum production of amylase, cellulase, and mannanase was obtained at an incubation temperature of 30oC, initial pH of 6.0, and NaCl concentration of 5% (w/v). Out of the tested agro-wastes, wheat bran was most suited for the production of amylase, corncob was optimum for cellulase production, and maximum mannanase yield was obtained using copra meal. Amylase and cellulase production was optimal at 96 hours of incubation, whereas mannanase required 144 hours of fermentation to reach its maximum activity. Conclusion: Aspergillus niger isolate L2S1 was capable of utilizing different carbon sources including cheap agro-residues as substrates for the production of halostable amylase, cellulase, and mannanase.