The effect has been described in a study published today in the journal Nature Geoscience.
"We know that when rivers dry up fish and insects die, and the whole food web of the river collapses," Febria said.
"However, we haven't previously appreciated the significance of all the decomposition that happens when the water comes back.
"The amount of carbon dioxide released in many cases is huge.
"We should all care about this because carbon dioxide in our atmosphere is the driver of global climate warming."
Febria said the new research indicated that increasingly drying rivers, along with other land use changes, were contributing to global climate warming.
"Moreover, climate warming in many places like Canterbury is predicted to increase the frequency and magnitude of drought which could also cause more river drying," she said.
"That is a real worry because that could form a positive feedback cycle by releasing even more carbon dioxide."
The paper was the first piece of research published from a wider collaborative study that involved 94 international partners from 22 countries studying the dry beds of 212 rivers from round the world, including Canterbury.
Such extensive global research efforts had traditionally been rare, and that a large group of international researchers had come together was "really quite significant", McIntosh said.
"I didn't really expect the magnitude of emissions to be quite so high, so the findings really should force a rethink of how the global carbon models are made so that they include CO2 emissions from intermittent rivers."