Use two shoes
Safety shoes are very good at resisting water no matter what the conditions are, but that doesn’t mean you should test its limits. Now manufacturers will invite you to do that, what have they got to lose? Most shoes are built to last, but even you know that there is a breaking point for everything. Use your safety shoes judiciously and keep two pairs on rotation. That way you will not overstress just one pair more than it can take.
Beeswax
Using beeswax to waterproof your shoes is fast becoming a fairly common technique these days and for the right reasons. Apply a coating of beeswax and let it melt down to the pores with a blow dryer, by the time the wax has settled in, you will have a comprehensive water protection. Mind you, this will only last a few days at most and to keep it effective for long you will have to reapply it.
Over the counter products
There are great products that you buy from off the shelves and apply them to your safety shoes for added waterproofing protection. These cost a little but the overall protection you will get from doing that is worth the investment. Try out a few of these products and see what fits you best.