This is important, says John, because temperature is a key driver of run-away plant growth in waterways.
"Excessive plant growth is because of nutrient run-off and sunlight. A shady stream won't get the algae response that drives changes in habitat.
"Farmers can mitigate a lot of the impact of farming by controlling the amount of light getting into the stream."
The vegetation is also useful to filter the run-off that is trying to get into the stream, he says.
"In the past 15 years there has been a huge improvement [in waterways protection].
Farmers in the Waikato have fenced off about 90 per cent of streams wider than a stride.
"On dry stock farms a lot less has been done, but the change has been led by the industry - there is still a long way to go, and it is good to see moves in the right direction."
John says NIWA and various regional council are monitoring about 1000 sites to detect trends in contamination.
"More sites had positive trends for contaminants, [exhibiting] better water clarity, because of reduced dissolved reactive phosphorus, ammonia and E.coli. Other sites are getting worse for nitrogen [N], which goes through the groundwater."
He says plants can take up N into their biomass at the land/water interface.
Trials using woodchip filters had helped the denitrification process as the microbes in the woodchip use oxygen in the N compound, eventually releasing the unwanted N as a gas.
"We are trialling this on a 9ha block in Southland: 10 by 10 metres to a depth of half a metre. We are losing almost all of the N before it gets into the drain."
The study is also using lime and crushed oyster shells as a filter of phosphorus.
"It depends on the soils too. Some have greater N-binding attributes. You could spread it back onto the farm."
When deciding what to plant, choose local wherever possible, says John. The local regional council will be able to advise what to plant, matched to the land form and wetness.
Stabilise the banks, and use sedges, trees and grasses as filters on the other side.
"These can be productive riparian buffers. You could take hay in the summer, and leave them as a filter in the wet. You could get firewood, or plant manuka for honey."
Farmers should actively manage the plantings to remove sequestered carbon from the system.
He says shading drains and streams can also make them faster running and increase their drainage capacity.