Seasonally fluctuating water levels, known as ‘flood pulses’, control the productivity of large river fisheries, but the extent and mechanisms through which flood pulses affect fishery yields are poorly understood. To quantify and better understand flood pulse effects on fishery yields, this study applied regression techniques to a hydrological and fishery record (years 1993–2004) for 42 species of the Amazon River floodplains. Models based on indices of fishing effort, high waters and low waters explained most of the interannual variability in yields ( R ² =0.8). The results indicated that high and low waters in any given year affected fishery yields two and three years later through changes in fish biomass available for harvesting, contributing 18% of the explained variability in yields. Fishing effort appeared to amplify high and low water effects by changing in direct proportion to changes in fish biomass available for harvesting, contributing 62% of the explained variability in yields. Although high waters are generally expected to have greater relative influence on fishery yields than low waters, high and low waters exerted equal forcing on these Amazonian river-floodplain fishery yields. These findings highlight the complex dynamics of river-floodplain fisheries in relation to interannual variability in flood pulses.