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Hi and thank you for your question.
This sounds like you have a slow speed circuit clogged in the carb. Water craft carbs have high speed and low speed circuits so since it runs normally at higher RPM's, this becomes the prime suspect.
I would suggest removing the carb and inspecting the low speed circuit. You can start by checking the setting for the low speed screw. It is the screw that is on the same side of the carb as the throttle cable. If it is set properly, then pull the diamond shaped steel plate off, remove the diaphragm, the "body1" which is like a half moon shaped piece of aluminum, and find the low speed jet under it. The low speed jet is the one that is physically in the lower of the 2 jets in the carb body.
Here is a link to a parts diagram that you can see what you are getting into:
The Body 1 is reference #24 and the low speed jet is reference # 19, the low speed screw is reference #35. You are looking for any kind of physical restriction. Use contact cleaner to blow through the passages and make sure they are clear. You will want to remove the low speed screw to blow through that as well. Before you do remove it, turn it in until lightly seated and count the turns in and write it down. You will need to reset the screw later.