To unravel the importance of zoosporic fungi in their participation in the cycling of organic matter and humification processes in aquatic ecosystems, this study was conducted to show the biodiversity and seasonality of zoosporic fungi, as well as their potential to degrade several polymeric materials. Using the baiting technique, twenty-nine species related to seven zoosporic fungal genera were collected during four seasons (autumn 2021–summer 2022) from the Nile River (from Helwan and El-Manial regions) and irrigation canals (El-Ismailia and El-Ibrahimia Canals) in Egypt. Some physicochemical parameters of water were evaluated in correlation with zoosporic fungi's occurrence, diversity, and seasonality. Out of isolated fungal taxa, only one species is related to one genus of true zoosporic fungi (i.e., Allomyces). In contrast, twenty-eight species are related to six genera of stramenopiles fungi (i.e., Achlya, Aphanomyces, Dictyuchus, Phytophthora, Pythium, and Saprolegnia). The Principal Coordinates Analysis (PCoA) was applied to reveal the correlation between the determined abiotic factors and particular species occurrence. The Shannon and Simpson indices were used to estimate species diversity, and fungal dominance and evenness were assessed to illustrate the richness of the recovered fungal taxa. The current study represents the first research concerning the survey, biodiversity, and seasonality of zoosporic fungi in most of the experimented water bodies. The most prevalent isolate, Achlya ambisexualis, was selected for molecular identification and tested for its potential to produce cellulase, amylase, protease, lipase, and asparaginase. This study remarkably suggests producing asparaginase (anticancer) utilizing the experimented fungus for the first time.