Anthropogenic dewatering of aquatic habitats can cause stranding and mortality of burrowed larval lampreys; however, the effects of dewatering have not been quantified. We assessed: (a) changes in spatial distribution, abundance, and emergence of larvae dewatered at Leaburg Reservoir (OR); (b) emergence and mortality of larvae dewatered in a laboratory; and (c) bias, precision, and interpretation of field results by simulation and modeling of laboratory results. In the field, we examined the distribution, abundance (by N‐mixture model), and density of larvae by electrofishing at randomly selected sites before dewatering and after refill, and assessed the emergence rate by observation and excavation during dewatering. Due to dewatering in the field, about 42% of larvae emerged and spatial distribution changed toward sites dewatered less than 20 hours. Estimated average density decreased from 10.8 larvae/m² before dewatering to 2.3 larvae/m² after refilling, suggesting that abundance declined by 79%; simulation suggested this decline ranged 71–84% (interquartile range). In the laboratory, we examined the emergence and mortality rates of larvae dewatered 0–48 hrs. The emergence rate in the laboratory was similar to that in the field. Mortality rate increased with hours dewatered and was higher for emerged than burrowed larvae. Laboratory estimates of mortality rate predicted a 61% decline in abundance if only burrowed larvae survived and a 54% decline if both burrowed and emerged larvae survived. Abundance declines in the field could be from mortality (e.g., desiccation, predation) and relocation to watered habitat. Our results indicate dewatering can substantially affect spatial distribution and abundance of larval lampreys in freshwater ecosystems.