As human activities intensify and global climate change accelerates, floodplain lakes are experiencing hydrological transformations that profoundly impact their ecology. Based on an extensive review of published literature, current knowledge of floodplain lakes and links between hydrology and ecology are summarized and synthesized. River-lake interactions determine hydrological conditions in floodplain lakes, with high spatial heterogeneity influenced by topography, geophysical properties, and climate. Seasonal fluctuations in water level and hydrological connectivity affect the community structure of aquatic organisms and biogeochemical processes. The interplay of floods and terrain shapes vegetation dynamics. Hydrological regimes sustain the quantity and quality of habitats, along with food resources for waterbirds and other organisms. Although certain species have adaptive capacities to changing hydrology through life history strategies, behavioral modifications, or physiological adjustments, long-term pressures from reservoir construction, intensive land use, and other human activities appear to be inducing cumulative, non-linear impacts that may push these ecosystems towards critical thresholds. Sustained pressures increase the risk of regime shifts, threatening ecosystem functionality. Current research often overlooks the complex interactions and feedbacks within ecosystems, leading to uncertain predictions regarding species resilience and ecosystem function. Existing methods are insufficient for fully integrating both short-term disturbances and long-term pressure. Advancing understanding of species adaptations across different temporal scales remains a priority, highlighting the need for more comprehensive frameworks for biodiversity conservation that effectively account for changing environment. Future efforts should focus on comprehensive in-situ monitoring and observation strategies, jointly with the application of advanced mathematical models, to enhance our understanding of ecology of floodplain lakes.