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Many environmental factors impact plant and pollinator communities. But variation in soil moisture and how it mediates the plant–pollinator interactions has yet to be elucidated. We hypothesized that long-term variation in soil moisture can exert a strong selective pressure on the floral and vegetative traits of plants, leading to changes in pollinator visitation. We demonstrated that there are three phenotypic populations of Gentiana aristata in our study alpine region in the Qinghai-Tibetan Plateau that vary in floral colour and other traits. Pink (dry habitat) and blue (intermediate habitat) flower populations are visited primarily by bumblebees, and white (wet habitat) flower populations are visited by flies. These patterns of visitation are driven by vegetative and floral traits and are constant when non-endemic plants are placed in the intermediate habitats. Additionally, the floral communities in different habitats vary, with more insect-pollinated forbs in the dry and intermediate habitats versus the wet habitats. Through a common garden and reciprocal transplant experiment, we demonstrated that plant growth traits, pollinator attractiveness and seed production are highest when the plant population is raised in its endemic habitat. This suggests that these plant populations have evolved to pollinator communities associated with habitat differences.This article is part of the theme issue ‘From floral chemistry to landscapes: the natural processes influencing pollinator health’.