Bacteria have different capabilities for using nutrients depending on the form (e.g., inorganic vs. organic) and the N:P molar ratio. To experimentally address these potential effects, enclosures were placed in a wetland and amended with N and P in different forms (organic and inorganic) and in different N:P molar ratios. The bacterial communities were examined using fluorescent in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE), looking at total bacteria and alpha-, beta-, and gamma-proteobacteria and Cytophaga-Flavobacteria. FISH showed that bacterial abundance varied with the form of nutrients added, but did not with the stoichiometric ratio. DGGE also showed community changes with variation in nutrient form, but not as much with stoichiometry. In contrast to other groups, beta-proteobacteria showed no changes; this is an opportunistic and diverse group, and are likely able to grow under many conditions. Nutrients enter aquatic systems from many sources, including fertilizers, and, not only the concentration of nutrient that is added to the system but what form it is in can have important effects on the bacterial community. However, stoichiometry appears to play little role in determining community composition.