Accurate estimates of contaminant loads in flowing water are necessary to meet regulatory requirements and investigate effects on biota, but they may be strongly influenced by sampling regime. We report how sample timing and frequency influence suspended sediment load estimates in a 5th order river in SE Idaho. We compare daily load estimates calculated using 30-min discharge and sediment concentration data, set-time (1000 h) sampling at frequencies of 1-28 days, and estimates based on monthly water quality sampling. At base flow, load estimates were typically lowest in the afternoon, with diurnal variation of up to 50%. Estimates using daily average and daily set-time data differed from estimates using 30-min data by up to 32% and 16%, respectively. Deviations in load estimates increased as sample frequency decreased, with deviations of more than 10% when sample frequency exceeded 4 days. Loads derived from monthly water quality sampling consistently underestimated best estimates by up to 50%. Deviations in load estimates were not consistently greater during the typical runoff period compared to the remainder of the year. Our results provide specific guidance for estimating sediment loads, and are relevant to other water body stressors (e.g., nutrients, toxics, organics) that are associated with sediment.