Nanoparticles (NPs) continue to be extensively produced by many industries, which ultimately leads to its release into the aquatic environment. It is crucial to estimate the impact of low concentrations of NPs which are environmentally relevant. Litter decomposition is a key ecological process in forested streams; microbes like fungi and bacteria are recognised to play a vital role in litter decomposition. In this study, zinc oxide (ZnO), titanium dioxide (TiO), silver loaded ZnO (Ag/ZnO) and silver loaded TiO (Ag/TiO) NPs were synthesized, and impacts of low concentrations (0, 2.5, 25, 50 μM) on leaf litter decomposition, fungal sporulation and bacterial growth were assessed. Fungal assemblages consisting of Articulospora tetracladia, Neonectria lugdunensis, Tricladium splendens and Varicosporium elodeae were used to study litter decomposition in microcosms exposed to NPs for 21 days. Two freshwater bacterial species belonging to the family Enterobacteriaceae were used to assess growth after 12 h of exposure to NPs. Types and concentrations of NPs affected litter decomposition and sporulation but not growth of bacteria. Leaf mass loss was significantly different between all concentrations but not between 25 and 50 μM. Fungal sporulation was significantly different among all concentrations of NPs. Fungal sporulation decreased with increase in concentration of NPs whereas a particular trend was not observed with mass loss except for Ag/ZnO. A 50 μM of Ag/ZnO had the highest impact on litter decomposition while 50 μM of ZnO on sporulation. The impact of Ag loaded metal oxides were not strikingly different from those of bare metal oxides except for the more pronounced impact on the mass loss accomplished by Ag/ZnO than by ZnO. Overall our study highlights that very low concentrations of NPs in freshwaters can impact freshwater ecosystem functioning.