Seasonal discharge programs, which take advantage of temporal variation of stream assimilative capacity, are cost effective. However, these seasonal discharge control programs should not increase the risk of water quality violations. A method is presented to estimate the allowable pollutant loads under both seasonal and non-seasonal discharge control programs for a single discharger that maintains the same level of risk of water quality violation. An enhanced in-stream water quality model QUAL2E-UNCAS was applied to a 39-km river reach of the Des Moines River below Des Moines Sewage Treatment Plant (DMSTP) in Iowa. The model was calibrated for dissolved oxygen (DO), biological oxygen demand (BOD), and ammonia as nitrogen with standard errors of 10, 17, and 23% by comparing with the observed water quality data. Monte-Carlo simulation technique was then implemented for seasonal and non-seasonal discharge program to assess the water quality violation risk and the allowable pollutant load. The results indicated that the four-seasonal program offers about 136% increase in BOD loading and 61% increase in ammonia loading when compared with the non-seasonal program without any increase in the violation probabilities, whereas the two-seasonal program only offers 13% decrease in BOD loading and 56% increase in ammonia loading. It is found that the multi-discharge program was beneficial for both water quality indicators, and thus provides a way of reducing the overall cost of waste treatment.