Spartina alterniflora decomposition is an important route for carbon transfer to estuarine detrital food webs. The two major microbial groups of decomposers are fungi and bacteria, both studied separately in the Spartina decay system. By using flow-through microcosms, we studied how fungi affect Spartina decomposition products and how bacteria respond to the addition of these products as growth substrates. We found that fungi do not significantly alter leaf characteristics over < 40 day incubations, but fungi decrease Spartina particle removal and immobilize leached dissolved organic carbon (DOC), nitrogen, and phosphorus. Bacteria grown on these fungally-modified leachates did not respond numerically. However, bacterial operational taxonomic unit (OTU) diversity and ribotype diversity decreased with fungal influence. Leachates from fungally-modified Spartina leaves enhanced the relative proportion of alpha-Proteobacteria, the major Spartina-associated ribotype in nature. Overall, however, there was no conclusive evidence for antagonism between fungi and bacteria in the Spartina decay system.