As far as I know, property taxes are calculated according to the individual home's assessed value. The characteristics of a neighborhood can boost or lower a home's value (proximity to schools, shopping, parks, density, etc), so the taxes would also vary, even if the home itself is comparable.
Don't lose too much sleep on the Mississippi River's flood potential. The entire length of Dubuque's waterfront is protected by a 30-foot high flood-protection barrier, and has been since 1972. The highest recorded level of flooding EVER in the city's history was 26.81 ft., and that was in 1965. The highest level since then was 25.40 ft., in 2001. Most of the wall is buried beneath a dirt levy, disguising it from public view. In the unlikely event that water overtops the wall, most of the areas that would be directly affected are non-residential. More info:
Advanced Hydrologic Prediction Service: Quad Cities: Mississippi River at Dubuque (Railroad Bridge)
The highest levels of fear about flooding pertain to sporadic flash-floods that occur from time to time, and revolve around the Catfish Creek and Bee Branch Sewer Line, NOT the Mississippi River. Without getting into too much detail... I can tell you that these problems are being addressed as well. (Google "Bee Branch Creek Restoration")
People in Dubuque just don't worry about the Mississippi flooding, and it's NEVER a consideration when buying a home in the city. Good luck to you, and welcome to Dubuque!
