The three main disadvantages of UV are: (1) high cost of operation, (2) anything which will prevent the UV light from reaching the bacteria will prevent an effective kill, and (3) UV light tends to ionize compounds and break them apart (i.e. nitrate could become nitrite in UV light), causing toxic effects on the effluent. Suspended solids, slime growth, turbidity, and color are some of the factors which have an adverse effect on UV disinfection.

http://water.me.vccs.edu/courses/ENV149/ultraviolet.htm