A fundamental, yet little‐explored, question is if climate change has affected niche relationships and spatial associations of native non‐invasive species in established local communities, potentially affecting interspecific interactions and community organization. Here, long‐term (1991‒2020) changes in habitat niche overlaps (HNOs; measured in terms of three habitat categories describing the amount and development of shore vegetation and shore depth) and spatial associations (SAs; measured as co‐occurrence on lakes) were studied in relation to climate‐driven changes in habitat phenology in a community of eight migratory waterbird species breeding on 37 lakes in southeastern Finland. Overall timing of ice‐out date (IOD) and within‐season variation in the timing of ice‐out (standard deviation of IOD, SDIOD) in lakes determine habitat (lake) availability for waterbirds during the settling phase. Previous work has documented that IOD has advanced and SDIOD increased during 1991‒2020, with species responding differently to these changes in their habitat use. HNO and SA varied considerably in the 28 species pairs of eight species during the study period. The effect of IOD and SDIOD on that variation was generally small, effect sizes differing from zero only in eight out of 112 cases. However, the direction and magnitude of the effects of IOD and SDIOD on HNO and SA varied considerably among the species pairs. Although not statistically significant, overall differences in the direction and magnitude of the effect sizes suggested that the impacts of IOD and SDIOD on HNO and SA were stronger in species pairs in which the species were more similar in terms of settling phenology, and stronger for early settling species than for late settling species. Observed changes in niche relationships probably reflect changes in interspecific interactions and affect the possibilities for heterospecific information use in habitat selection.