Water balance measurements can be used to estimate seepage rates from animal waste lagoons and earthen storages. This method requires detailed measurements of depth changes and cumulative evaporation during 5- to 10-d periods. Quantifying the uncertainty surrounding the measurements is crucial if data from seepage tests are used to determine if lagoons are meeting engineering specifications and operating within regulatory guidelines. Uncertainty analyses, using a 95% confidence interval, were applied to field data collected during studies of animal waste lagoons in Kansas and Oklahoma. Changes in depth were measured with float-based recorders and evaporation was estimated from meteorological observations. Results showed that rate changes in depth could be measured to within +/-0.28 mm d(-1) or better when wind speeds at the start and end of the test were less than 4 m s(-1). Uncertainty in evaporation was the most significant factor affecting the seepage estimate, and surface temperature and relative humidity were the main sources of imprecision in the evaporation calculations. Evaporation could be estimated to within 10 to 20%, with the largest uncertainty occurring during windy conditions. Uncertainty in the calculated seepage rate increased as evaporation increased. When evaporation rates are low (e.g., <4 mm d(-1)), seepage can be estimated to within +/-0.5 mm d(-1) with 95% confidence. A precision of +/-0.25 mm d(-1) is possible when research-grade instruments are deployed under favorable weather conditions. A measurement duration of 5 d is adequate for most water balance tests. In many cases, precision of the water balance technique will be sufficient in determining if a working lagoon is within regulatory guidelines.