River-floodplains support a significant number of small-scale capture fisheries despite having undergone degradation due to human modification of river flows by dams, pollution, and climate change. River fish production is underpinned by the annual flood-pulse and associated environmental changes that act as cues for spawning and dispersal for most species. However, studies on fish stock declines have focused more on overfishing than on hydroclimatic variability. Therefore, understanding how changes in flood-pulse variability influence fishing effort and yields is critical to inform adaptive fisheries’ management. We investigated hydroclimatic factors driving floodpulse variability and fish catch–effort dynamics in India’s Ganga River over two decades (2000–2020). We compiled fishers’ narratives of changing fish catches through semi-structured interviews to compare them with our observed trends. Flood amplitude showed increasing variability, longer duration, and earlier rise timings, linked to La Niña and El Niño phases. Catches per unit effort were correlated with total yield and effort but did not decline as fishers thought, despite overall declines in yield over time. Hydroclimatic variability was a more significant driver of changing yields than local fishing pressure. Rising uncertainty in fisheries’ production, in response to increasing flood-pulse variability and altered flows in the Gangetic Plains, may be affecting fishing behaviour and underlying resource conflicts.