Humber Rescue, which is run entirely by volunteers, said it had been an “exceptionally busy” period for its crews.
In a social media post, it said a team was called out by the Coastguard to help with a search on Saturday morning.
The service said a crew set out again on Saturday evening to assist a yacht near Spurn Point which had a “serious electrical fire”.
The volunteers returned home at 23:00 BST but were called out again in the early hours to another incident that did not finish until 05:00.
Eight swimmers were due to take part in the swimming event on Sunday, which was due to start at 07:30.
The Humber Swim starts from the Barton-upon-Humber side of the estuary.
The swimmers cross the estuary, under the Humber Bridge, and end near Humber Rescue’s base at Hessle.
Depending on the tide, the swim covers between 1.5km and 4km (about 1 to 2.5 miles).
Scholes said: “It’s a fantastic event and we’ve had great pleasure organising it.
“I feel very sad about stepping down.”
Scholes said the first swim, which she completed with 26 other swimmers 12 years ago, was “horrendous”.
“The waves were so high, the tide didn’t turn, and it’s just one of those things where you think, ‘am I going to get out of this?’
“But, luckily, we did, and we’ve come back for the last 12 years.”
As many as eight swims have been held each summer.
“I do feel very sad,” Scholes said.
“I’ll miss the Humber Rescue and all of the swimmers and the friends, but they’ve done an amazing job and raised over £130,000 in the 12 years.”
Scholes said she hoped the event would continue with new organisers.
“It’s a fantastic event, and we’ve had a great pleasure doing it,” she added.
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