1.1. Ocean Acidification and Upwelling Systems
 The atmospheric carbon dioxide (CO2) concentration is currently approaching 400 ppm, a level unparalleled over the last 0.8 million years [Lüthi et al., 2008]. About a quarter of the anthropogenic CO2 released during the last few decades has been taken up by the ocean [Canadell et al., 2007]. Following ocean uptake, CO2 forms carbonic acid which dissociates readily leading to a decrease in pH and carbonate ion (CO32−) concentration, which determines the calcium carbonate (CaCO3) saturation state (Ω) of the ocean. Atmospheric CO2 levels could potentially rise to 800 ppm by the end of the century, resulting in a further decrease in pH of up to 0.3 units and a 50% reduction in the concentration of CO32− and the saturation states of CaCO3 minerals [Orr et al., 2005]. The overall response of marine organisms to ocean acidification remains uncertain [Langer et al., 2006, 2009; Ries et al., 2009]. However, laboratory studies suggest that at least some species of marine calcifiers will be negatively affected [Comeau et al., 2009; Fabry et al., 2008; Kuffner et al., 2008; Langer et al., 2006].
 The surface ocean is generally oversaturated with respect to calcite and aragonite, the most common types of biogenic CaCO3. On a global scale, surface CaCO3 saturation states show a latitudinal gradient which roughly follows sea surface temperature (SST) distributions. This is mainly due to the fact that cold water can hold more CO2 (because of increased solubility) and that dissolved CO2in most of the surface ocean is at near-equilibrium with the atmosphere [Opdyke and Wilkinson, 1993]. Calcium carbonate saturation states are therefore highest in low latitude waters and decline toward the poles. Low SST combined with high freshwater inputs [Yamamoto-Kawai et al., 2009] have defined polar oceans as ocean acidification “hot spots” which is why a large number of ocean acidification studies have focused on these regions [Anderson et al., 2010; Bates and Mathis, 2009; Chierici and Fransson, 2009; Comeau et al., 2009; Steinacher et al., 2009; Yamamoto-Kawai et al., 2009]. Recent evidence, however, suggests that the effects of ocean acidification can also be pronounced at lower latitude locations where cold, deep, CO2-rich water upwells to the surface ocean. Along the west coast of the U.S.A., for example, seasonal upwelling processes now bring waters undersaturated with respect to aragonite (Ωarag < 1) to the surface over the continental shelf [Feely et al., 2008; Hauri et al., 2009]. Even though Pacific deep waters naturally hold higher concentrations of CO2, mainly from organic carbon mineralization, Feely et al.  calculated that if the anthropogenic signal was to be removed from the CO2 content of the upwelled water, the aragonite saturation horizon would be 50 m deeper. As the CaCO3 saturation horizon continues to shoal in the next decades, upwelling areas will be among the first to experience the impacts of CaCO3 undersaturation.
 Although marginal seas are net exporters of organic carbon, their role in inorganic carbon cycling remains ambiguous [Gattuso et al., 1998]. This is because in these systems, and especially in upwelling areas, inorganic carbon cycling is driven by a combination of biological and physical processes including the production and remineralization of organic carbon and biogenic carbonates, upwelling of nutrients and dissolved inorganic carbon, and water mass mixing [Borges and Frankignoulle, 2001]. In such dynamic systems carbonate chemistry data from fixed time series stations falls short in distinguishing between biological and physical signals [Bakker et al., 1996; Borges and Frankignoulle, 1999; DeGrandpre et al., 1998; Friederich et al., 1995]. In contrast, Lagrangian studies, such as the one described here, allow for biological processes to be studied independently from physical processes (i.e., tidal advection, water mass mixing etc.). This study provides insight into the mechanisms and processes involved in inorganic carbon cycling in eastern boundary upwelling systems and along upwelling filaments.
 During the last two decades a number of studies have focused on inorganic carbon cycling in upwelling systems but mainly of the Pacific Ocean [Fassbender et al., 2011; Feely et al., 2008; Ianson et al., 2003; Ribas-Ribas et al., 2011; Torres et al., 2011; van Geen et al., 2000]. In contrast, very little carbonate chemistry data exists from the Atlantic Ocean except from the Benguela [Santana-Casiano et al., 2009] and Galician [Borges and Frankignoulle, 2001, 2002] upwellings. Upwelling systems are typically rich fishing grounds, and because of the ecological and socio-economic importance of these waters, their response to ocean acidification must be addressed.
1.2. The Mauritanian Upwelling Region
 The Mauritanian upwelling region is one of the two major upwelling systems in the Atlantic Ocean and globally one of the most biologically productive ecosystems, supporting large commercial fisheries [Pauly and Christensen, 1995].
 The hydrography of the upper tropical northeast Atlantic Ocean is complex [Stramma et al., 2005]. Major currents in the area include the Canary Current (CC), which flows in a southwesterly direction from the Canary Islands. The upwelling of cold, nutrient-rich waters takes place along the coastline caused by alongshore wind stress. The position and intensity of the Mauritanian upwelling follows closely the seasonal variations in the intensity and spatial characteristics of the trade winds. During the winter, the trade winds are positioned furthest south between 10°N and 25°N. During spring the wind system migrates northward and in summer is positioned between 20°N and 32°N. In the region between 20°N and 25°N (the location of this study) the trade winds and associated upwelling remain strong and persistent throughout the year [Stramma et al., 2005].
 Here we describe the carbonate system dynamics within an upwelling filament in the Mauritanian upwelling area based on direct measurements of dissolved inorganic carbon (DIC) and total alkalinity (TA). Previous studies of biogeochemical dynamics in upwelling regions [Joint et al., 2001; Wilkerson and Dugdale, 1987] have utilized drifting buoys to track upwelled water. This method, however, has the limitation that one can never be certain that the drifting buoys remain within the upwelled plume. Buoys released together in patches of upwelled water often tend to follow tracks which diverge over time [D'Asaro, 2004], so it is uncertain if deployed buoys stay with the initial patch of water. In this study, the tracer sulphur hexafluoride (SF6) was used to accurately follow the path of the upwelled water during its migration offshore and to constrain rates of horizontal and vertical mixing. The use of this tracer allowed a more accurate determination of the effects of upwelling on biogeochemical processes and carbonate chemistry.