Here a new analytical methodology is described for measuring the isotopic composition of boron in foraminifera using multicollector inductively coupled plasma mass spectrometry (MC-ICPMS). This new approach is fast (~10 samples analysed in duplicate per analytical session) and accurate (to better than 0.25 per mil at 95% confidence) with acceptable sample size requirements (1-3 mg of carbonate). A core top calibration of several common planktic and two benthic species from geographically widespread localities shows a very close agreement between the isotopic composition measured by MC-ICPMS and the isotopic composition of B(OH)-4 in seawater (as predicted using the recently measured isotopic equilibrium factor of 1.0272) at the depth of habitat. A down core and core top investigation of boron concentration (B/Ca ratio) shows that the partition coefficient is influenced by [CO2-3] complicating the application of this proxy. Nevertheless, it is demonstrated that these two proxies can be used to fully constrain the carbonate system of surface water in the Caribbean Sea (ODP Site 999A) over the last 130 kyr. This reconstruction shows that during much of the Holocene and the last interglacial period surface water at Site 999A was in equilibrium with the atmosphere with respect to CO2. During the intervening colder periods although the surface water pCO2 was lower than the Holocene, it was a minor to significant source of CO2 to the atmosphere possibly due to either an expansion of the eastern equatorial Atlantic upwelling zone, or a more local expansion of coastal upwelling in the southern Caribbean. Such reorganisation of the oceanic carbonate system in favour of a larger source of CO2 to the atmosphere from the equatorial ocean may require mechanisms responsible for lowering atmospheric CO2 during glacial periods to be more efficient than previously supposed.