Climate change and human activities are expected to have a major impact on the structure and functioning of marine ecosystems and the biogeochemical cycles they mediate in the coming years. Here we describe time series measurements of biogenic bromocarbons (CHBr3 and CH2Br2) collected in coastal waters of the western Antarctic Peninsula which is one of the world's most rapidly changing marine environments. Our measurements spanned a period of changing sea-ice dynamics and phytoplankton community structure driven by climatic forcing. Specifically, the occurrence of high chlorophylla concentrations (≥5 μg L−1) and dominance of the largest phytoplankton size fraction (≥20 μm) indicating diatom bloom conditions was reduced following winter periods with a relatively short winter sea-ice duration (<50 days). While large inter-annual variability in seawater CHBr3 concentrations was observed alongside these changes the same was not found for CH2Br2 which is surprising given their proposed common source. Seawater CHBr3 concentrations were found to be significantly higher (122 [14.7–580] pmol L−1, P < 0.0001, Mann-Whitney) in samples collected in diatom bloom compared to non-bloom waters (42.9 [12.0–126] pmol L−1). A comparison of sea-to-air flux rates suggests that a switch from diatom bloom to non-bloom conditions results in a factor of 3–4 decrease in average CHBr3sea-to-air emission rates which will reduce the supply of biogenic bromine to the atmosphere. Our calculations suggest that this will drive a decrease in inorganic bromine levels in the troposphere by a factor of 2–3 outside of ozone depletion events with potentially important implications for ozone cycling and dimethyl sulphide oxidation. This work has captured and crucially quantified the impact of a climate-induced change in a marine ecosystem on ocean-atmosphere biogeochemistry.