Water exchange unevenness (WEU) is defined as the coefficient of variation in water exchange intensity over time. Although its influence on aquatic plant characteristics has been recently investigated, there is limited understanding regarding the effects of this hydrodynamic change on submerged vegetation. This study investigated the impacts of WEU on the species dominance and community composition of submerged macrophytes in three bays with different WEU conditions in Erhai Lake, China. Subsequently, a laboratory experiment was conducted to elucidate the mechanisms underlying these effects. The field investigation showed that the dominance values of submerged macrophytes were influenced by WEU. As WEU decreased, the average dominance value decreased for Vallisneria natans (by 34.54 %), Myriophyllum spicatum (16.82 %), and Hydrilla verticillata (12.84 %); showed no significant change for Potamogeton lucens; and increased for Potamogeton maackianus (14.22 %) and Ceratophyllum demersum (17.52 %). The laboratory experiment showed that lower WEU markedly inhibited the growth of V. natans, slightly inhibited that of M. spicatum, and stimulated that of P. maackianus, consistent with the field observations. The inhibitory effect was attributed to a reduced concentration of carbon dioxide in the water; adaptive strategies, i.e., plant height, biomass allocation, and root traits, were more effective for M. spicatum than for V. natans. The stimulated growth of P. maackianus was attributed to increased dissolved oxygen concentration, which promoted root growth and nutrient uptake. Our results indicate that WEU has significant effects on the growth and community characteristics of submerged macrophytes.