The Arctic Ocean's sea ice loss dynamically impacts carbon uptake potential, as assessed through measured carbonate parameters, such as total alkalinity. In the open ocean, boron (B) is the third largest contributor to alkalinity via borate and is usually accounted for through the conservative boron to salinity ratio (B/S), and not directly measured. Here, we present findings on non-conservative boron dynamics, that results in significant B/S deviations, observed in ice melt zone waters, snow, slush, brine, and annual sea ice (n = 169) in the Fram Strait entering the Central Arctic. These samples were collected during the onset of the melt season on the 2023 ARTofMELT expedition, covering a wide practical salinity range (2–59). Barring snow, the average B/S ratio across the study was 0.1321 ± 0.0032 mg kg−1 ‰−1, similar to the mean B/S ratio measured amongst several polar water masses near Iceland, as well as the accepted B/S for other ocean regions. Results indicate minor deviations from accepted B/S ratios (indicating conservative behavior) across the sample practical salinity range and reflect an uncertainty in the borate contribution to total alkalinity of less than 2.9 μmol kg−1 at in-situ temperatures. B fractionation appears to occur during sea ice formation, causing greater B in the sea ice reservoir whereas brine, slush, lead, and under-ice water reservoirs are depleted in B. As such, under-ice and lead, brine, and slush samples all had measured B/S ratios (0.1305 ± 0.0011, 0.1305 ± 0.0018, and 0.1304 ± 0.0017 mg kg−1 ‰−1, respectively) lower than the established ratio whereas the average sea ice B/S ratio (0.1331 ± 0.0035 mg kg−1 ‰−1) was closest to accepted values (0.1336 ± 0.0005 mg kg−1 ‰−1). Arctic open ocean samples also had a lower B/S ratio (0.1304 ± 0.0014 mg kg−1 ‰−1). Our findings, together with a previous Arctic B ice study, suggest that B (probably in the form of B(OH)4−) is incorporated into authigenic CaCO3 minerals, replacing CO32− within the mineral lattice during sea ice formation. This process consequentially lowers the B/S ratio in the open Arctic Ocean, compared to the established global ocean ratio. Nevertheless, the incorporation of B into the sea ice reservoir does not fully account for the deficit of B in the Arctic Ocean samples, suggesting further accounting of B Arctic pathways is necessary. In future climate scenarios involving increased sea ice melt, the transition from multiyear to annual sea ice, permafrost thaw, and increased riverine discharge, the behavior of B in the Arctic Ocean is expected to become more dynamic.