This study examined the efficacy of marking wild populations of lampreys with visible implant elastomer (VIE) for 6–18 months to examine ammocoete movements using Cormack–Jolly–Seber (CJS) open‐population models. These methods were tested on two lamprey populations in different river systems. American brook lamprey Lethenteron appendix at Dyke Creek apparent survival (φ) was high in the summer and winter (c. 0·7), but declined after flow events in the spring and autumn. Sea lamprey Petromyzon marinus at Oquaga Creek φ in the top‐ranked models varied with stream location and time. Estimates of φ were similar to Dyke Creek during the summer (c. 0·7), but declined after flow events and remained low (c. 0·1) in winter. Open‐population models support current understanding of ammocoete movement, i.e. dispersal is driven by high‐flow events at certain times of the year. The present study provides a framework to study ammocoetes with VIE.