A good way to keep excess water and other objects from entering your boots is to wear gaiters. When you wear them use a shingling effect by putting your pant legs on the outside of the gaiters and the gaiters on the outside of the top of the boots. Wearing a pair of sock liners under your hiking socks can help ward off blister by reducing friction against your foot. When buying boots be certain that the salesperson is competent. Go to reputable mountain shops and avoid buying from catalogs unless you have no other place to go.
Footwear is a very personal purchase that contains many variables.
For great information on buying hiking boots read Colin Fletcher's The Complete Walker III . Always break in new boots before wearing them hiking. You should wipe your feet down twice a day for at least a week , two if possible, with rubbing alcohol. This toughens the skin helping to eliminate blisters. You should waterproof all boots, even those that claim to be waterproof, with some sort of waterproofing compound.