New Calabar River and the Omuihuechi Stream are important sources of water in Southern Nigeria. They receive urban contaminants and wastes from automobile and marine fuels, heavy oils, spent lubricants and other petroleum products, untreated sewage, human and animal faeces and various kinds of domestic, agricultural and industrial waste. The impact of human activities on the abiotic quality and mycoflora of the New Calabar River and the Omuihuechi Stream were investigated for a period of seven months. Sampling and measurements were conducted within three designated zones. Five sampling stations (A, B, C, D and E) along the course of the River are grouped in Zone I. Station F is in Zone II while station G (control) constitutes Zone III The samples were assessed for Temperature, Flow Velocity, Secchi-disc Transparency, Sulphate, Phosphate, Dissolved Oxygen, BOD, total organic carbon, Oil and Grease concentrations. The forest stream acidity (pH 5.33 ± 0.29) was not significantly different from the River acidity (pH 5.47±0.37). The River flow velocity was 0.213 ± 0.015ms1 . The following fungal genera were identified: Aspergillus, Byssochlamys, Candida, Cephalosporium, Cladosporium, Fusarium, Mucor, Penicillium, Rhizopus, Saccharomyces, Sporobolomyces and Trichoderma. Zone II was observed to show a high tendency of eutrophication than zone 1 while zone III (control) was free from such influences. There were significant differences in Fungal count, pH, Organic carbon, BOD5 and Transparency (P=0.01) between the Zones. The human activities occurring at specific points (stations) along the river course appear to have influenced both biotic and abiotic parameters of the aquatic ecosystem.