The weird thing is, I've found that as soon as anyone in my family gets the inside of their shoes wet, they start to stink. So, I have puddle/rain sandals and non-puddle/rain sandals for everyone. But you can reduce/eliminate the smell with Dr Scholls foot odor eater spray. It is called something like that, but you can spray the shoes before and after use to reduce the smell. Then I recommend scrubbing them once a week.
Also,never tried it, but I know people who do, you can put a quick swipe of deodorant on the feet to help eliminate smell too.