There had always been a sandbar at this particular bend in the Charles River, where Watertown and Brighton meet. About 20 years ago, Kane Larin realized it was getting bigger -- fast.

“It grew rather quickly over those years and it became quite a navigational hazard,” he says.

As a director of Community Rowing Incorporated, Larin watched that growing island eventually take up two-thirds of the width of the river. Rowers, paddlers and yachts from two nearby clubs had to hug the banks, sliding through a few inches of water, often lodging in sand and damaging boats. One woman’s boat was destroyed when she collided with another craft. Larin got Bob Zimmerman and the Charles River Watershed Association involved.

“We came out and took a look and everyone agreed – you know what, this is dangerous,” Zimmerman recalls.

The growing island wasn’t a natural phenomenon, he says. More waterways like the Charles are becoming clogged with sediment as climate change advances. Because of climate change, Boston’s getting more hard bursts of rain. And because we’re covering more of the ground, those hard bursts of rain aren’t falling on soil and getting soaked up. Instead the rain’s hitting pavement, and becoming fast-moving streams of runoff.

“And when you run off real fast you can carry a lot of stuff,” Zimmerman says. “The sand and salt that we put on roads in the winter time and that all flows out here. And you create this sandbar.”

The state worried disturbing the sandbar would disloge toxic materials that remain in the riverbed from the time when the Charles was used for industrial and sewage dumping.

“There was a relatively long period of lobbying to get to the place where everybody was comfortable with this thing coming out,” Zimmerman says.

The watershed association raised $70,000 to figure out how far down the sandbar went and what was in it. Julie Wood oversaw the project.

“So we did some investigations to see if anything was going on that was a smoking gun,” she laughs. Wood was looking for the reason “why so much sediment was coming out here.”

What she found was that Boston’s original landscape was reasserting itself. The sandbar was growing at the spot where a historic tributary joined the river.

“If you were here 300 years ago this would’ve been an open stream flowing into the Charles,” Wood says.

That open stream – the Fanieul Brook -- no longer exists; Zimmerman says it’s been erased by development and concrete. But fast-moving runoff still collects in the same pathways, bringing an increasing amount of sediment to the river. DCR commissioner Leo Roy says, luckily, that material wasn’t toxic.

“Fortunately the material was mostly sand, silt and organic material. A few bricks thrown in,” he says.

So after five years of lobbying and research, the state spent $800,000 to removethe sandbar this winter. In a matter of days it was sucked up into a mile-long pipe and dumped onto a DCR parking lot. The sediment was spread out to dry across an area bigger than a football field before it was trucked off.

“State governments with our budget today can’t do it alone and so really everything we’re looking for are partnerships with nonprofits and others to really get these great things done,” Roy says.

Runoff will probably become a bigger and bigger expense for Roy’s department… The EPA is starting to step up regulation of storm water after pressure from advocates who say the sediment problem and flooding is just going to get worse as climate change advances. Next year new EPA permits go into effect – they’re aimed at pushing local government to reduce runoff by installing more permeable surfaces or rain gardens.

As the new permitting requirements come forward, we’ll have to focus as well on those areas,” Roy says. Asked about the potential cost of such measures, he says, “I’m always worried about the cost of these things because if we put money in one area, we take it from someplace else.”

But if runoff isn’t slowed, Zimmerman says the Charles River sandbar may be back and bigger than ever.

“Until we come up with method of slowing down runoff this will fill in over time,” he says. “The question is how long. It’ll probably be between 10 and 50 years, but who knows.”

If that happens, the state may have to spend hundreds of thousands of dollars to remove the sandbar – again.