Freshwater ecosystems, among the most biodiverse on Earth, are increasingly threatened by emerging contaminants, such as antibiotics and engineered nanoparticles. Ciprofloxacin (CIP) and silver nanoparticles (Ag-NPs) enter aquatic environments primarily through inefficient wastewater treatment, making freshwater systems their ultimate repository. These contaminants can disrupt key ecosystem processes, such as organic matter decomposition driven by microbial communities like aquatic hyphomycetes. In this study, eco-sustainable chitosan–niobium oxide nanocomposite membranes (CS–NbO) were developed, characterized, and applied as a novel remediation strategy for the removal of CIP and Ag-NPs, both individually and in combination. The membranes were successfully synthesized and characterized, using contact angle measurements, scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy–attenuated total reflectance (FTIR-ATR), and SEM–energy-dispersive X-ray (SEM-EDX). Results showed increased hydrophilicity and distinct structural modification following crosslinking, supporting their suitability for contaminant adsorption. Dynamic light scattering (DLS) analysis confirmed the stability and low polydispersity of Ag-NPs in aqueous media. CS–NbO membranes were further evaluated through biological assays assessing oxidative stress responses in fungal communities. Activities of antioxidant enzymes, including catalase and glutathione S-transferase, increased in microcosms exposed to untreated CIP and/or Ag-NPs, indicating induced oxidative stress. In contrast, these responses were significantly reduced in microcosms treated with CS–NbO membranes. Leaf litter decomposition was not significantly affected. Overall, our findings highlight that CIP and Ag-NPs pose potential risks to aquatic fungal communities and ecosystem functions. Importantly, CS–NbO nanocomposite membranes emerge as eco-friendly materials to mitigate the impacts of emerging contaminants in freshwater ecosystems.