Freshwater inflows can deliver substantial inputs of allochthonous organic carbon to estuaries. The role that allochthonous DOC has on structuring bacterial and phytoplankton communities is still not well understood. We performed a series of 1.25 L bioassay limitation experiments on the Bega and Clyde River estuaries in NSW, Australia, examining what resources limit bacteria and phytoplankton growth. We hypothesized that during base flow conditions bacteria would be carbon limited, and after high flow conditions they would be nutrient limited. A full factorial design was used with additions of carbon (glucose), nitrogen (KNO3) and phosphorus (KH2PO4). During the experiments that took place during base flow conditions bacteria were always primarily C-limited. After high flow conditions, bacteria were P-limited on the Clyde River, and remained C-limited on the Bega River. Phytoplankton growth was limited at all times in each estuary, tending toward N-limitation on the Bega River and P-limitation on the Clyde river. During high flow conditions on the Clyde River, when bacteria and phytoplankton were both primarily P-limited, it appeared that bacteria was able to outcompete phytoplankton for nutrients. These results suggest that freshwater inflows and allochthonous DOC maybe important in structuring estuarine microbial ecosystems and individual estuaries may behave differently in terms of their limiting resources.