The picture of bacterial biofilms as a colloidal gel composed of rigid bacterial cells protected by extracellular crosslinked polymer matrix has been pivotal in understanding their ability to adapt their microstructure and viscoelasticity to environmental assaults. This work explores if an analogous perspective exists in fungal biofilms with long filamentous cells. To this end, we consider biofilms of the fungus Neurospora discreta formed on the air-liquid interface, which has shown an ability to remove excess nitrogen and phosphorous from wastewater effectively. We investigated the changes to the viscoelasticity and the microstructure of these biofilms when the biofilms uptake varying concentrations of nitrogen and phosphorous, using large amplitude oscillatory shear flow rheology (LAOS) and field-emission scanning electron microscopy (FESEM), respectively. A distinctive peak in the loss modulus (G″) at 30–50 % shear strain is observed, indicating the transition from an elastic to plastic deformation state. Though a peak in G″ has been observed in several soft materials, including bacterial biofilms, it has eluded interpretation in terms of quantifiable microstructural features. The central finding of this work is that the intensity of the G″ peak, signifying resistance to large deformations, correlates directly with the protein and polysaccharide concentrations per unit biomass in the extracellular matrix and inversely with the shear-induced changes in filament orientation in the hyphal network. These correlations have implications for the rational design of fungal biofilms with tuneable mechanical properties.