Climate change has substantially impacted global runoff patterns and biodiversity, yet the response of river biodiversity to future runoff changes remains unclear. Here, we project and characterize this evolution by calculating the Shannon index (SI), a measure of river biodiversity, for 32 major rivers worldwide under future climate scenarios. We find that historically, SI has generally decreased for most rivers (88%), but future projections suggest an overall increase, albeit with values generally lower than those observed historically. Under different Shared Socioeconomic Pathways (SSPs) - SSP1-2.6, SSP3-7.0, and SSP5-8.5 - SI is expected to decrease by 53%, 66%, and 66%, respectively, reflecting altered runoff patterns. The most substantial decrease is projected under SSP3-7.0. Predictions indicate that biodiversity in the majority of rivers will decline notably in the second and third quarters of the 21st century, with some potential for recovery in the final quarter. These findings highlight an escalating threat to river biodiversity globally, posing significant challenges to ecosystem health and integrity.