The impact of green-synthesised mosquitocidal nanoparticles on non-target aquatic predators is poorly studied. In this research, we proposed a single-step method to synthesise silver nanoparticles (Ag NP) using the seed extract of Melia azedarach. Ag NP were characterised using a variety of biophysical methods, including UV–vis spectrophotometry, scanning electron microscopy, energy-dispersive X-ray spectroscopy and Fourier transform infrared spectroscopy. In laboratory assays on Anopheles stephensi, Ag NP showed LC50 ranging from 2.897 (I instar larvae) to 14.548 ppm (pupae). In the field, the application of Ag NP (10 × LC50) lead to complete elimination of larval populations after 72 h. The application of Ag NP in the aquatic environment did not show negative adverse effects on predatory efficiency of the mosquito natural enemy Cyclops vernalis. Overall, this study highlights the concrete possibility to employ M. azedarach-synthesised Ag NP on young instars of malaria vectors.