•We examine changes in distribution, occurrence and bloom incidence of the noxious Gonyostomum semen.•G. semen was spreading in southern Sweden but not north of Limes Norrlandicus.•The occurrence of G. semen was mainly explained by climate variables (e.g. temperature).•pH and water color were the best predictors of bloom incidence.•Morphometry and catchment variables were only important at high dominance levels of G. semen (>90% total phytoplankton biomass).