Arsenic (As) is a naturally occurring metalloid element widespread in the environment. Assessing the ecological risk of As in surface water, especially the acute risk caused by emergent pollution incidents, is of great significance. However, acute toxicity data including median lethal concentration (LC50) and median effective concentration (EC50) of As derived by toxicology experiment may vary according to the exposure time, which is referred as time dependence effect. Time dependence not only affects toxicity data but also influences the characterization of acute risk in the ecosystem. However, previous research on the time dependence effect of As, especially the quantitative influence on the risk assessment is still limited. In this research, acute toxicity data of As(III) and As(V) was collected. Time dependence of toxicology data of inorganic As was studied. Time-dependent species sensitivity distributions of freshwater species were established. The hazardous concentration for 5% of species (HC5) values in different exposure time were further derived. Finally, the dynamic ecological risk of As in major Chinese water basins was evaluated. The results suggested that the toxicity data of inorganic As had a significant linear relationship (p < 0.01) with time. The HC5 values of As (III) and As (V) at an exposure time of four days were reduced by 15.5% and 77.5%, respectively, as compared to the HC5 value of one day. According to the ecological risk characterized by the probability density overlapping area method, the ecological risk of As(III) and As(V) increases with the exposure duration. The Yangtze River had the highest risk, with risk values ranging from 19.9% to 22.6%. According to the results, the time dependence of toxicity data should be fully considered in the formulation of water quality criteria or ecological risk assessment so as to provide better protection for the water ecosystem security.