Please keep in mind that the "smell" of the lagoon being opened has to do with decayed organic matter, mainly the tree leaves that have fallen in the water. The tannin in the leaves is what gives it the color and odor. It is not harmful, just a contrast to the pristine color and neutral odor of the water. There is also fish, bird, croc, iguana and other creatures poop, but mainly organic matter.
Because the waves bring up the sand and create a dam, there is a build up of the water and it sits there and does it's thing.
One solution would be to keep the lagoon mostly open so there was not a build up of the water. That said, it wouldn't be as good for the lagoon since the natural cycle is what we experience.
So if you want to mess with Mother Nature so that your olofactory and visual senses are not offended, let's keep the lagoon open. It would be easy to do.
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