Measurement of excretion rates are an important component of assessing the role of animals in biogeochemical cycles. However, incubation times vary among excretion studies and the potentially important effects of starvation and handling stress are often assumed to be minimal. As a step towards standardizing field procedures in excretion studies, we determined the effects of handling stress and incubation time on excretion rates of NH₄-N in representative aquatic groups, including fishes, unionid mussels, snails, crayfishes, and aquatic insects. Excretion rates in 2 treatments were monitored every 15 minutes for 2 hours: treatment 1 was incubated immediately (no pre-starvation) while treatment 2 was starved for 2 hours before incubation began. This design allowed us to distinguish starvation effects on NH₄-N excretion rates from those of handling stress. Data for the snail Elimia cahawbensis indicated no effect of handling stress but a clear effect of incubation time on excretion rate, presumably due to starvation. Standard methods will facilitate more accurate measurement of excretion rates by aquatic organisms. Such accuracy is needed if our understanding of the relative importance of excretion in nutrient cycles is to be improved.