The "unexpected" co-funding arrangement will allow upgrades to some of the council’s flood protection schemes and covers 75% of the costs.
Environment Southland will fund 25%.
Meanwhile, the Otago Regional Council is waiting for the Ministry of Business, Innovation and Employment to finalise its $5 million funding agreement, before it can begin community consultation.
Environment Southland chairman Nicol Horrell said the $13.875million funding was "fantastic" and would help cover work in Invercargill and the Mataura and Waiau catchments.
"[It] means we can improve flood defences that would have taken us 10 years or more to achieve through our regular work programme, for a quarter of the cost."
The work was also estimated to create more than 100 jobs in Southland in the next few years.
The total cost of the projects — which included rock work on the Mataura stop banks, upgrading and extending the stop bank at Boundary Creek upstream of the Mataura township and buying a new pump for the Lake Hawkins pump station on Stead St, near Invercargill Airport — is $18.5million.
The council will contribute $4.625 million.
"As the government’s funding was unexpected, the council is planning to use existing reserves of up to $1.5 million for this year [2020-21]," Mr Horrell said.
The remaining $3.125 million would be consulted on next year for the 2021-31 long-term plan.
Options for how to fund that were likely to include reserves, a targeted rate and borrowing, he said.
Consultation for the council’s upgrade of flood protection schemes is open until 5pm on November 9.
Otago Regional Council operations general manager Gavin Palmer said despite its funding not yet being finalised, a "significant" amount of planning for four projects had been done and the planning process was now complete.
The projects, which were all existing flood protection projects, were a contour channel upgrade in West Taieri, repairing flood erosion and scour in part of the Clutha River, upgrading and installing flow management structures at Robson Lagoon, and a weighting blanket in Outram to reduce the risk of floodbank failure and flooding.
"The community information and consultation will be the priority once the agreement has been finalised," he said.
It was expected to be finalised early next month and work on the ground was expected a few months after that.
The time to complete each project ranged from 12 months to 36 months.
