Wayne Ives, a stream flow specialist at the department, said his agency is working with water users in the Isinglass River watershed to protect the river's health.
John Magee, a biologist at the New Hampshire Fish and Game Department, said fish habitats are in danger, as are businesses that depend on spending by hunters, anglers, and wildlife watchers.
"As human population grows, we suck up water," Magee said. "At some point, we dry up the streams."
Magee said he was unaware of any rivers in New Hampshire that had dried up because of development. However, he said, such problems have been documented elsewhere.
Jennifer Jacobs, an associate professor of civil engineering at the University of New Hampshire, said the Ipswich River in Massachusetts is a prime example: Water withdrawals have been so heavy that the river dried up at times during the summer.
"It's hard for any aquatic creature to sustain itself," she said.
The University of New Hampshire is helping study the effect of water withdrawals on the Lamprey and Souhegan rivers as part of a state effort to develop water management plans. Jacobs said the state also needs to update its laws and set standards for surface and groundwater withdrawals.
A draft of the report on the Souhegan River, released last month, called for measures to protect the river's flow levels. State records date to 1934, and although river flows are affected by dams, the seasons, and the weather, the lows are getting lower over time, Jacobs said.
"There is definitely a concern in the region," she said.
Even when rivers don't dry up, lower flows mean warmer temperatures, endangering species that need colder water to survive.
Ives and Jacobs both said a loss of funding for US Geological Survey stream flow gauges has made it more difficult to predict which rivers and streams are at risk and collect data on long-term changes.
"We don't have a very good direct way to measure what's going in the rivers, and it makes it difficult," Ives said.
Trout Unlimited, a Virginia-based nonprofit, released a report last month warning that heavy water use was endangering rivers in New England . Residential development is the main culprit, but bottled water companies, ski resorts, and farmers are also heavy water users, the report said.
"We're noticing in the whole width and breadth of New Hampshire, there is an effect on flow rates," said Dave Magnon, chairman of Trout Unlimited's New Hampshire council.
