The successful establishment of invasive species has been shown to depend on aspects of the invaded community, such as gap characteristics. Biotic resistance may be particularly critical for stopping invaders at early life history stages, but new species can often invade following disturbances, which may create microsites with very different characteristics than are usually present. We examine the response of two invasive thistle species, Carduus nutans L. and C. acanthoides L., to three different microsite characteristics: disturbance type, size, and water availability. The two species initially responded differently to the type of disturbance: C. acanthoides had higher emergence and survival in plots with both above- and belowground disturbance, whereas C. nutans had better early performance in large microsites with above-ground disturbance only. Later in their life cycle, C. nutans performed better in plots that had been disturbed both above- and belowground, whereas C. acanthoides was largely unaffected by disturbance type. Increased emergence and survival, larger size and a higher proportion flowering were observed in larger gaps for both species throughout the life cycle. Watering had a negative impact on C. nutans emergence and fall survival and on C. acanthoides survival to the following summer. Overall, these results suggest that disturbance-generated microsite characteristics (disturbance type and size) may have large impacts on establishment of these two Carduus species, which in turn may persist well beyond the initial stages of growth. Studying invader responses to disturbance can help us to understand under what circumstances they are likely to establish and create persistent problems; avoiding or ameliorating such situations will have significant management benefits.