Disturbances that alter cross-habitat food web linkages can lead to whole-scale changes to aquatic systems. In coastal rivers of the Everglades (Florida, U.S.A.), increases in rainfall inundate adjacent floodplains, providing habitat for floodplain fish and macroinvertebrate species. In the dry season, rainfall decreases and floodplains dry, forcing floodplain prey into these river systems. These prey provide a prey subsidy for an estuarine predator, the common snook (Centropomus undecimalis). In 2011, severe drought impacted the region, likely affecting this prey subsidy. In this study, we ask (i) did the 2011 drought affect the magnitude and composition of floodplain prey subsidies to the common snook? and (ii) if species composition changed, were there energetic differences between the pre- and post-disturbance prey species? Results showed that 1 year after the drought, subsidies to the common snook decreased by 75%. On top of that decrease in overall flux, diet composition of the common snook switched from floodplain fishes to drought-tolerant floodplain macroinvertebrates. Lastly, energetic analyses showed that these postdrought macroinvertebrate prey subsidies had 43% less calories than floodplain fishes. Our findings illustrate the importance of considering not only the biomass that transfers from one food web to the next, but also how the species composition of the subsidy may affect incorporation into recipient food webs.