Abstract. Multiyear drought has been demonstrated to cause non-stationary rainfall–runoff relationship. But whether this change can occur in catchments that have also experienced vegetation change and whether it invalidates the most widely used methods for estimating impacts of vegetation change – i.e., the paired-catchment method (PCM), the time–trend method (TTM), and the sensitivity-based method (SBM) – on runoff is still unknown and rarely discussed. Estimated inconsistent afforestation impacts were 32.8 %, 93.5 %, and 76.1 % of total runoff changes in the Red Hill paired experimental catchments in Australia during the period of 1990–2015 by the PCM, TTM, and SBM, respectively. In addition to afforestation, the Red Hill paired experimental catchments have experienced a 10-year drought (2000–2009) and have been demonstrated to lead to non-stationary rainfall–runoff relationships of paired catchments. Estimated impacts of vegetation change by the PCM (32.8 %) is still reliable and is not invalided by multiyear drought-induced non-stationarity, because the PCM can eliminate all impacts by different factors on paired catchments (multiyear drought and climate variability), except the purposed treatment (afforestation). For the TTM and SBM, traditional application did not further differentiate different drivers of non-stationary rainfall–runoff relationship (i.e., multiyear drought and vegetation change), which led to significant overestimation of afforestation effects. A new framework was further proposed to separate the effects of three factors on runoff changes, including vegetation change, climate variability, and hydroclimatic non-stationarity (i.e., multiyear drought). Based on the new framework, impacts of multiyear drought and climate variability on runoff of the control catchment (Kileys Run) were 87.2 % and 12.8 %, respectively. Impacts of afforestation, multiyear drought, and climate variability on runoff of the treated catchment (Red Hill) were 32.8 %, 54.7 %, and 23.9 %, respectively. Impacts of afforestation on runoff were 38.8 % by the TTM and 21.4 % by the SBM, agreeing well with that by the PCM (32.8 %). This study not only demonstrated that multiyear drought can induce non-stationary rainfall–runoff relationship using field observations, but also proposed a new framework to better separate the impact of vegetation change on runoff under climate-induced non-stationary condition. More importantly, it is shown that non-stationarity induced by multiyear drought does not invalidate the PCM, and PCM is still the most reliable method even though the control catchment experienced climate-induced shift in the rainfall–runoff relationship.