River-floodplain fisheries are highly productive as seasonal water level changes, known as ‘flood pulses,’ increase the productivity of fish populations by providing them with feeding and reproductive opportunities in the floodplains. However, current understanding of flood pulse effects on fisheries activities at seasonal and interannual time scales remains deficient. Here, we analyze a comprehensive dataset of the Lower Amazon region to address the following questions: How flood pulses affect river-floodplain fishing strategies with respect to species composition and habitat? What is the interannual lag of hydrological effects on fisheries yields? And does that lag depend on the life-history strategy of the target fish species? A principal coordinates analysis indicated that fishing activities followed a clear seasonal pattern characterized by alternating habitat and species. Cross-correlation analyses indicated the existence of positive effects caused by mean water levels on fish catches roughly two or three years later. The lag of such water level effects on fish catches was proportional to species longevity, being 22 months for short-lived species with a mean age at catch of 21 months, 26 months for medium-lived species with a mean age at catch of 27.2 months, and 42 months for short-lived species with a mean age at catch of 33.7 months. The results of this study highlight the large seasonal and annual variability of tropical river-floodplain fisheries, and underscore the dependence of fish catches on natural river hydrological cycles. Because these fisheries are suffering increasing exploitation pressures, conservation measures are necessary to protect the hydrology of Amazonian rivers.