The Quill Lakes Watershed Association says a lack of provincial money could force it to close without ever finding a solution to flooding.
The two have worked together in the past to find ways to keep the saline lakes from overflowing, but recent proposals from the association did not get funding.
The Quill Lakes are terminal, without a natural spill outlet, and lake levels began to rise in 2005.
Each year, runoff events and rain contributed to higher levels.
Significant rain and rising levels occurred in 2010, followed by the flood of 2011 that hit much of southern Saskatchewan and parts of Manitoba.
By 2018, the lakes had risen seven metres, flooded agricultural land, roads and highways, and put a major railway at risk.
One economic study pegged losses between 2012 and 2018 at $253 million.
