In this work, we investigate the potential application of a novel biogenic ZnO nano-photocatalyst (NPc) for the sustainable photocatalytic recycling and reuse of aquaculture wastewater. The ZnO nanostructures were synthesized via a green chemical precipitation method using an aqueous solution of non-toxic precursors (dried extract of the edible mushroom Cyclocybe aegerita (V. Brig.) Vizzini 2014 and zinc acetate) under mild conditions by stirring at 80 °C for two hours with pH adjusted to 12 using 2 M NaOH. The resulting flower-like ZnO NPc was characterized using High-Resolution Scanning Electron Microscopy, X-ray Diffraction, UV–Vis Diffuse Reflectance and Fourier Transform Infrared Spectroscopy confirming its nanostructured morphology, crystalline phase, and functional group interactions. The unique properties, including the appropriate valence and conduction band redox potentials make this biogenic ZnO NPc a promising candidate for photocatalytic control of (de)nitrification in recirculating fish farming systems. The conditions for successful simultaneous (de)nitrification of nitrite and ammonia in a simple two-stage photocatalytic experimental setup were investigated. This mushroom-mediated synthesis not only enhances the environmental compatibility of the NPc but also supports circular bioeconomy principles. Our findings propose a cost-effective, environmentally friendly, and efficient solution for managing nitrogen species in fish farming effluents, contributing to cleaner aquaculture practices and sustainable water resource management.