Global ecosystems face mercury contamination, yet long-term data are scarce, hindering understanding of ecosystem responses to atmospheric Hg input changes. To bridge the data gap and assess ecosystem responses, we compiled and compared a mercury accumulation database from peat, lake, ice and marine deposits worldwide with atmospheric mercury deposition modelled by GEOS-Chem, focusing on trends, magnitudes, spatial-temporal distributions and impact factors. The mercury fluxes in all four deposits showed a 5- to 9-fold increase over 1700-2012, with lake and peat mercury fluxes that generally mirrored atmospheric deposition trends. Significant decreases in lake and peat mercury fluxes post-1950 in Europe evidenced effective environmental policies, whereas rises in East Asia, Africa and Oceania highlighted coal-use impacts, inter alia. Conversely, mercury fluxes in marine and high-altitude ecosystems did not align well with atmospheric deposition, emphasizing natural influences over anthropogenic impacts. Our study underscores the importance of these key regions and ecosystems for future mercury management. This study compiled a global mercury accumulation database from natural deposits and compared it with modelled atmospheric deposition, revealing significant regional differences in mercury flux trends. This study highlights the importance of targeted environmental policies for effective mercury management in the future.