Water got into the engine.
If you have driven through a large amount of water, to the point where the engine has inhaled water, the engine may have been damaged. It is possible that only some basic maintenance services alone may fix your issue; I would strongly recommend having the air filter and the engine oil changed by a mechanic. Once these services have been done, the engine may run ok and have no issues.
If other issues exist, internal engine parts, possibly the whole engine, may require replacement. A good inspection of the engine should indicate it's condition.
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