Restoration of habitats often necessitates the eradication of exotic animals from a specified area. One of the many challenges associated with the removal of introduced animals is determining the distribution and continued presence of individuals in order to efficiently target control operations and minimise any adverse effects associated with removal. We examined the feasibility of using environmental DNA (eDNA) from water samples, relative to more traditional electric fishing, netting and spotlight surveys (i.e., visual observations of the small streams at night), to determine the presence of brown trout. Samples were taken from within the Zealandia Sanctuary near Wellington, New Zealand, before and after treatment with the piscicide rotenone. Using filtration of water samples, we successfully extracted brown trout DNA from water both before and after rotenone treatment. In most cases, DNA presence corresponded to results obtained through netting and spotlight surveys, and in one instance detected the continued presence of trout in a treated stream (which was subsequently confirmed). We conclude that the use of environmental DNA to detect the presence of exotic fish can be a useful tool to assist in the assessment and restoration of aquatic habitats.