We investigated the effects of river floodpulses on the water chemistry and diatom assemblages in a floodplain wetland. During the two year study period (November 2003–September 2005), the river and wetland exhibited three periods of surface hydrologic connectivity. The impacts of flooding depended on flood magnitude and duration. Both the long/high magnitude and short/high magnitude floods thoroughly mixed river and wetland waters, with conductivity, total nitrogen, and total phosphorus in the wetland decreasing to levels similar to the river. In contrast, the short/low magnitude flood did not mix water chemistry. Wetland conductivity, total nitrogen, and total phosphorus remained elevated. Changes in algal biomass followed changes in water chemistry with the high magnitude floods producing conditions unfavorable for algal growth. Algal biomass decreased in the wetland coinciding with the two high magnitude floods. Increases in algal biomass coincided with the short/low magnitude flood. Wetland and river water column diatom assemblages were dominated by periphytic taxa. The diatom assemblage in the river and wetland were distinct, except during the short/high magnitude flood. During this period, floodwaters brought diatoms into the wetland and both systems were dominated by planktonic centric taxa. Similar diatom taxa were observed in the wetland water column assemblage and the assemblage collected in settling chambers, although their relative abundances varied. Shifts in the settling diatom assemblage coincided with periods of flooding, indicating that river floodwaters leave a discernable signal within this assemblage. Our findings indicate that caution should be exercised when using diatom-based bioassessment in frequently flooded wetlands as the wetland diatom assemblage is influenced by river floodwaters and changes may depend on the duration and magnitude of flooding.