Councillors yesterday approved the inclusion but not without some concern.
''It's come back to bite us,'' Cr Martin McPherson said.
''A hundred thousand dollars is a lot of coin and it's only going to grow.''
Speaking after the meeting, council chief executive Phil Melhopt said the money would not just fund maintenance of those two trails but others in the district.
He said options on giving out the money were yet to be discussed but funds could be allocated on a case-by-case basis.
He also did not know if the money would be set aside each year, or if it was a one-off.
The Roxburgh Gorge and Clutha Gold trails were, from the start, intended to be self funding and the trusts behind them developed maintenance contribution tags, at $25 each or $50 per family for a year's worth of access to both trails.
When the tags were announced, shortly before the October 24 opening of the trails last year, Roxburgh Gorge Trail Trust chairman Stephen Jeffery said the intention of the tags was not only to help fund maintenance but ensure the costs for doing so would not come back on ratepayers.
''We're not asking ratepayers to fund maintenance. We're asking users to be community spirited and fund their usage,'' he said.
Maintenance for the trails was estimated by the trusts to cost $50,000 to $100,000 per trail per year.
Just over a year ago, Mayor Tony Lepper said trail trusts should not think of the council as a backstop for maintenance funding. He told the Clutha [river] management committee, then a separate committee, it might be the ideal group to look at the district's tracks and [wondered] whether there needed to be a management plan.
''My observation is that [trail] trusts are going to struggle for maintenance funding in the future and the backstop way will be to come back to councils, community boards and this [Clutha management] committee to maintain these assets.''
The Clutha management committee has been rolled into the community services committee, but the $100,000 is to come from the Clutha management account.
That account is funded by ratepayers from the Cromwell, Alexandra and Teviot wards, but not Maniototo.
At the council meeting yesterday, Mr Lepper said it was time to ''debate this whole new brave world we are heading into''.
Deputy mayor Neil Gillespie said the idea raised the question of why the Clutha management account was to fund these trails when individual community boards funded other trails.
''We need some consistency ... we can't keep doing it piecemeal.''
Cr Steve Battrick said it went without saying that pressure would be applied to central Government to stump up with the funds alluded to by Prime Minister John Key at the opening of the Roxburgh Gorge and Clutha Gold trails.
Cr Jeffery said he thought if council was seen to be supporting the trails, central Government might be more likely to pitch in.
Mr Key alluded to ''likely'' central government funding for trail maintenance under a new national governance board for such trails.
He said trail trusts would still need to contribute some costs. Mr Melhopt said the $100,000 was based on $1000 per km of trail, the money was only a provisional amount, and the council was aware there were other trails, both existing and forthcoming, that might need funding help. The council already funds maintenance of the Millennium Trail, between Alexandra and Clyde, at three times that rate.
He said the trail trusts had not formally asked the council for financial help, ''but we know that ultimately there will need to be some funding''.
People will get a chance to voice their opinions on the matter when the council's annual plan goes out for consultation in April.
