Salt marshes along the northeastern coast of the United States are increasingly subject to changes in hydrology and enrichment with nitrogen as a result of human activities. We conducted a greenhouse experiment to determine the response of Phragmites australis, Spartina alterniflora, and their root-associated microbial communities to these environmental perturbations. Two sets of treatments were compared: 1) saturated versus drained hydrology under low N enrichment and 2) low versus high N enrichment under drained hydrologic conditions. Unvegetated sediments were planted with either Phragmites australis or Spartina alterniflora, and after one growing season, sediment characteristics, macrophyte biomass, and sediment microbial community structure, as described by phospholipid fatty acids (PLFAs), were analyzed. Under all conditions tested, Spartina root production was significantly greater than Phragmites. While Spartina invested more biomass in roots, Phragmites invested proportionally more biomass in shoots and rhizomes, and Phragmites response to drained hydrology or to an increase in N also differed from that of Spartina. Under N enrichment, the rate of Phragmites stem production doubled, and under drained conditions the ratio of Phragmites shoot:root biomass increased, while Spartina biomass ratios remained unchanged. Although Spartina root biomass was significantly greater than that of Phragmites, under drained conditions the Spartina sediment PLFA diversity was significantly lower than the PLFA diversity in both Phragmites and unvegetated sediments. Under saturated conditions, vegetated sediments exhibited greater PLFA diversity, while no diversity differences were seen in unvegetated sediments under the two hydrologic conditions. Six PLFAs were responsible for 80% of the separation seen within the Principal Components Analysis ordination space. Significant differences in these PLFAs were due to hydrology when comparing saturated vs. drained sediments, and predominantly due to the plant species when comparing N treatments under drained conditions. Our results suggest that macrophyte root association can influence the structure of estuarine sediment microbial communities, but that saturated hydrological conditions may override the plant influences.