Freshwater ecosystems have been degraded due to intensive freshwater abstraction. Therefore, environmental flow requirements (EFRs) methods have been proposed to maintain healthy rivers and/or restore river flows. In this study, we used the Variable Monthly Flow (VMF) method to calculate the transgression of freshwater planetary boundaries: (1) natural deficits in which flow does not meet EFRs due to climate variability, and (2) anthropogenic deficits caused by water abstractions. The novelty is that we calculated spatially and cumulative monthly water deficits by river types including the frequency, magnitude and causes of environmental flow (EF) deficits (climatic and/or anthropogenic). Water deficit was found to be a regional rather than a global concern (less than 5% of total discharge). The results show that, from 1960 to 2000, perennial rivers with low flow alteration, such as the Amazon, had an EF deficit of 2–12% of the total discharge, and that the climate deficit was responsible for up to 75% of the total deficit. In rivers with high seasonality and high water abstractions such as the Indus, the total deficit represents up to 130% of its total discharge, 85% of which is due to withdrawals. We highlight the need to allocate water to humans and ecosystems sustainably. This article is part of the Royal Society Science+ meeting issue ‘Drought risk in the Anthropocene’.