The effects of water quality on wetland-associated bacterial communities exposed to high inorganic phosphorus (P) concentrations by studying rhizoplane, rhizosphere and water microbial communities were examined using mesocosms planted with either Phalaris arundinacea or Veronica anagallis-aquatica. Mesocosms were exposed to high or poor water quality treatments for 91 days before receiving a 5 mg/L pulse of P (P2O5), and were sampled until 49 days after exposure (DAE). Structural community characteristics were determined using PCR-DGGE banding patterns from 16S bacterial DNA. Functional changes were assessed from carbon source utilization profiles (Biolog™ Ecoplates). Microbial communities differed in their response to P loading. Rhizoplane communities showed the most significant changes to structural and functional characteristics, while rhizosphere communities exhibited the least. A combination of factors including water quality and plant species influenced rhizoplane community structure post-P loading (repeated-measures REML P ≤ 0.05), while structural and functional diversity declined significantly, independent of the treatment (P ≤ 0.001). The results of this study indicate that environmentally relevant levels of inorganic P can have significant effects on wetland-associated microbial communities, however, these effects are dependent on the bacterial community being monitored. Water quality and plant species may play a secondary role in determining these effects.