In water quality management, pollution control strategies have been sought to accord with the assimilative capacity of water bodies so as to preserve water quality. The waste load allocation (WLA) is a useful approach to determine the allowable loading of pollution sources in water quality management. For any WLA, a particular water body condition is needed as a basic scenario under which the relevant parameters are fixed. The particular flow rate is known as design flow and usually set at low flow in order to be protective. The design flow is traditionally a particular deterministic value, such as Q (75), implying that it is expected that the probability of water quality violation is 25% in the long run. However, this long-term expectation might not be realized in individual years due to variability of natural flow. The flow variability will make a WLA plan overoptimistic or over-conservative in different years, suggesting that the deterministic design flow without uncertainty consideration might lead to an ineffective or inefficient decision-making. To address the problem, we explicate the relationship between flow variability, design flow and water quality with different flow distributions to facilitate the understanding of the process of a WLA. In order to manifest the uncertainty effects of design flow, the results from the annual flow duration curve (AFDC) is compared with the conventional flow duration curve (FDC). The AFDC approach is capable of obtaining the uncertainty level of the design flow by generating the confidence interval rather than a fixed value. The effect of different record lengths on design flow determination is estimated as well. Finally, a refined WLA process is proposed with a re-examination of water quality violation to improve the allocation decision under uncertainty. TaHan River Basin in northern Taiwan is used as a case study.