The aquatic ecosystem harbours a variety of micro-organisms, among which water-borne conidial fungi occupy an important place. Their occurrence in freshwater habitat has great significance in the decomposition of submerged plant materials, nutrient release and productivity. Their occurrence and frequency to extreme temperatures and pH may have a profound effect on fungal community composition and metabolic activities. The present paper deals with the diversity of conidial aquatic fungi from different unexplored freshwater bodies flowing through different elevations (1000-1500 m) in district Nainital, Kumaun Himalaya. Comparative study of species composition in different seasons, sporulation temperatures and pH conditions was also carried out. In all, 18 species of conidial fungi belonging to 14 genera were recorded, out of which maximum species (11 species) were recorded in both rainy (July to September) and winter seasons (November to December). Anguillospora crassa, Beltrania rhombica, Campylospora chaetocladia, Cylindrocarpon aquaticum, Helicomyces roseus and Tetracladium setigerum were isolated only during rainy season; Alatospora acuminata, Clavariopsis aquatica, Clavatospora tentacula, Lemonniera pseudofloscula, L. terrestris and Tetrachaetum elegans were isolated only during winter season while Lunulospora curvula, L. cymbiformis, Setosynnema isthmosporum, Tetracladium marchalianum and Triscelophorus acuminatus were isolated in both rainy and winter seasons. The preferred pH and the sporulation temperature ranged from 6-7 and 15-20 °? respectively. The results of the present study are clearly indicating fungal species composition variations along pH, temperature, seasonal and altitudinal gradients and the sites selected for this exploratory investigation are being undertaken for the first time.