Buy some waterproof over shoes. I plan to buy a pair soon, most likely a model made by Endura.

Both the Dexter and the Luminite fit both MTB and road shoes using different style cleats (off the product info).
http://www.endurasport.com/Dept.aspx?dept_id=107

I have cycling boots to handle cold and wet weather over the winter. But with warmer weather or when the forecast unexpectedly changes, an overshoe would be welcome insurance.

Last Tuesday, I was totally caught off guard and unprepared. Sunny skies heading to work turned into serious rain by my late night 14 mile commute home. The rain never stopped and it took several days to get the shoes dry.