Environmental stochasticity is important in explaining the persistence and establishment of invasive species, but the simultaneous effects of environmental and demographic factors are difficult to separate. Understanding how demography and environmental factors affect invasive species abundance over large temporal and spatial scales is essential to anticipate populations at risk of becoming established and setting appropriate management measures. Using a hierarchical mixed modeling approach we analyzed the spatial and interannual dynamics of the invasive raphidophyte Gonyostomum semen, a noxious flagellate which is spreading in northern Europe, in response to demographic and environmental variation. We used data from 76 lakes distributed across two biogeographical regions in Sweden (Central Plains in the south and Fennoscandian region in the north) and sampled during 14 years. We found a strong asynchrony in the density dynamics of G. semen populations between the two regions. G. semen showed positive trends (i.e. increasing frequency of high density peaks) in most southern lakes, forming established populations with recurrent blooms in successive years in some of them. In contrast, G. semen populations were smaller and more stochastic in the north. G. semen previous year's abundance, a proxy for cyst production and recruitment, had a strong control on the dynamics, likely contributing to the stability of high density populations in southern lakes. Conversely, the effects of climate and habitat were weaker and their influence varied across regions. Temperature was the limiting factor in the north whereas local habitat was more important in the south. Synthesis: A full understanding of the mechanisms driving abundance changes across large scales can only be gained if endogenous and environmental factors are analyzed together. For phytoplankton species, and specially, noxious microalgae, this implies that proxies for cyst production and recruitment, which are the inoculum for next year population, should be included in e.g. distribution, bloom formation and climate models, as these may modify establishment and population response to environmental variation. Asynchronous changes in abundance across regions also indicate that management plans should be developed for small regions, as inference at a large scale may obscure the mechanisms driving local population changes.