In order to assess the change in spotted gar (Lepisosteus oculatus) density relative to water level in a disconnected low-water refuge, we used monofilament gill nets to collect adult gar throughout the annual flood pulse in the Atchafalaya River Basin (ARB), Louisiana. Spotted gar density was greatest during low-water periods and there was a strong negative correlation between spotted gar catch per unit effort and the Atchafalaya River water level at Butte La Rose (P = 0.0002, R2 = 0.5763). The spotted gar population in Deer Lake, a disconnected backwater area, was estimated to be 2,079 individuals (95% CL = 849 < N < 5,198) during a low-water period. Adult spotted gar biomass in Deer Lake at bank-full level was one of the highest recorded levels (267 kg ha-1; P [109 ≤ 267 ≤ 668] = 0.95) in a large river floodplain. Fall 2005 water levels in the ARB were among the lowest on record. During abnormally low-water years in disconnected habitats, high densities of top predators such as spotted gar may alter trophic food webs in backwater areas of large river floodplains. Mean water stage for the Atchafalaya River has decreased over the last few decades (P = 0.0002, R2 = 0.2615) due to down cutting of the channel, thus the size of the fish population carried over to the following year is partly dependent on the amount of water remaining during the low-water period. If water levels drop to extreme levels as in 2005, piscivory will likely reduce community abundance for the following year, and several consecutive years of extremely low flood pulses could significantly reduce fish population abundance in the ARB.