The Murray–Darling Basin (MDB) supports extensive water infrastructure, including thousands of pumps that divert water for irrigation, domestic use, and industry. However, these pumps entrain millions of native fish and crustaceans annually, potentially contributing to population declines. Fish protection screens have been proposed as a solution, but field-based evaluations in Australian systems are scarce. We assessed the effectiveness of modern fish screens at three pump sites across different riverine environments in the MDB. Unscreened pumps entrained multiple native fish species, including various life stages of the threatened eel-tailed catfish (Tandanus tandanus) and stocked juvenile Murray cod (Maccullochella peelii). Entrainment was reduced by 93–100% for fish and over 99% for debris at screened versus unscreened pumps. Screens were effective at both small- and large-scale diversions and across multiple native species. Our results show that well-designed and maintained screens can significantly reduce biotic losses, while allowing efficient water extraction. Fish screens should be considered a key tool in native fish conservation and sustainable water management.