The correct answer is D. It was pouring rain all afternoon so my garden of flowers and vegetables flooded.
By using the conjunction so, you are writing the result of the words before that very conjunction. In the case above, the result of the pouring rain is the flooding of flowers and vegetables.
A is incorrect because the semi colon in front of the conjunction is unnecessary; B is incorrect because just writing a comma creates a run-on sentence, which is grammatically incorrect; C is incorrect because there is a conjunction missing instead of a semi colon - thus, D is correct.