Not being an expert ,but having worked in the waste water treatment area for 30 years I will add my 2scents. We were at La Mananzanilla and were at the lagoon in question.
Will there be sewage infiltration ,likely yes especially in heavy rain seasons.
Can the smell be coming only from the lagoon, yes it's possible. The bottom of lagoons and swamps gather material over the years and could become feet thick ,eventually turning septic.you may even see bubbles coming up sometimes which is natural.these watercourses are a treatment system in them selves cleaning the water as it passes by.Sometimes when hydraulically overloaded they don't work so well( heavy flow).
So could there be sewage in the lagoon ,yes .Could the smell not be sewage ,yes.
I do realize there can always be infrastructure done but it may not eliminate the issue.
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