Geographic variation in intraspecific traits is a central subject in evolutionary ecology, yet the relative roles of historical, environmental, and biotic processes in shaping such variation are not well resolved. I investigated the drivers of large-scale flower color variation in the spotted bellflower (Campanula punctata), a widespread perennial herb native to northeast Asia that exhibits continuous variation in floral pigmentation due to differing levels of anthocyanin. Anthocyanins are multifunctional pigments that contribute to pollinator attraction through visual signaling and to physiological protection against environmental stressors such as ultraviolet radiation, drought, and temperature extremes. To quantify pigmentation across the Japanese archipelago, I compiled georeferenced flower photographs from a citizen-science platform, extracted standardized color metrics, and integrated these metrics into a latent anthocyanin index using confirmatory factor analysis. I then modeled geographic variation in pigmentation using a spatial Bayesian framework (SPDE–INLA) to partition the contributions of broad-scale spatial structure, contemporary environmental gradients (climate, topography, soil), and predicted pollinator pressure based on species distribution models for key bumblebee pollinators of C. punctata. The spatial random field accounted for the largest proportion of variance, indicating that historical dispersal limitation and geographic isolation strongly structure floral color patterns across the archipelago, but environmental factors such as aridity and elevation and pollinator suitability also exhibited significant associations with pigmentation after accounting for spatial autocorrelation. To identify deviations from these expected ecological and spatial patterns, I analyzed residual variation from the spatial model using generalized additive models (GAMs), testing for associations with anthropogenic factors while controlling for nonlinear effects of elevation, phenology, and geography. This analysis revealed that flowers occurring in densely populated areas were significantly darker than predicted by ecological and spatial predictors alone, with a strong nonlinear interaction between human population density and elevation, consistent with localized anthropogenic influence such as introgression from horticultural lineages. Finally, structural equation modeling (SEM) indicated that environmental gradients influence pigmentation both directly via physiological constraints (e.g., aridity, elevation) and indirectly by modulating pollinator habitat suitability, clarifying how abiotic and biotic processes jointly shape geographic patterns of floral color variation. These results demonstrate that broad-scale spatial structure, ecological gradients, biotic interactions, and recent human impacts act hierarchically to shape intraspecific floral trait variation in C. punctata.