Simon Millar from Sapphire Coastal Adventures has seen Merimbula Marina shallow before, but never as shallow as it was at the start of this year's whale watching season.
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He said sand moved in and around the entrance to the channel after an east coast low dumped a large deposit of sand on the area in late 2020.
"There's no way this boat could get in there, it just draws too much, it's just too dangerous," he said about boat Bubbles, a 24-metre powered catamaran.
Ideally he would like to see the channel dredged, but was not confident that move would ever happen. An alternative would be to build a protected marina entrance with a rock wall similar to Bermagui's Marina.
Although the Millars considered Eden Marina as an alternative to Merimbula, there was already another operator there and it lacked the facilities necessary, including their own pontoon to safely chart passengers.
They have been be running some tours from Eden, but the majority were from Bermagui. Tours have been chartered twice daily during the whale season that runs from August until mid-November.
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"Bermagui has been working well, we've still got a lot of our locals from Merimbula coming up, so it's been great," he said.
Running a boat out from Merimbula is not off the cards though. Mr Millar said they have a smaller 16-metre boat with capacity for 50 people, that would be able to operate during "the top of the tide", times that change daily.
"We're just finishing it off at the slips now, it's a shallow draft boat, it's just trying to work out how we're going to coordinate between running here and there as there's a little bit of distance between."
He said one of the barriers was manpower as he no longer had the staff due to COVID, but was working out logistics in the meantime.
"We will start back up at Merimbula at some point this season, it's just a matter of how we're going to do it."
Despite not being able to set an exact time, Mr Millar was confident they would have the chance to run Merimbula tours within the next few weeks.
Another exciting development for the eco-tourism business would be the inclusion of swimming with the seals tours heading out to Montague Island, known by the Yuin people as Barunguba, in summer.
Sapphire Coastal Adventures plan to supply wetsuits and snorkels to its passengers and run daily tours, not on, but around the island by boat.
"That will be good through the summer, the water is already good swimming temperature now, but it will get better," said Mr Millar.