As atmospheric emissions of S have declined in the Northern Hemisphere, there has been an expectation of increased pH and alkalinity in streams believed to have been acidified by excess S and N. Many streams and lakes have not recovered. Evidence from East Bear Brook in Maine, USA and modelling with the groundwater acid-base model MAGIC (Cosby <i>et al.</i> 1985a,b) indicate that seasonal and yearly variations in soil PCO<sub>2</sub> are adequate to enhance or even reverse acid-base (alkalinity) changes anticipated from modest decreases of SO<sub>4</sub> in surface waters. Alkalinity is generated in the soil by exchange of H<sup>+</sup> from dissociation of H<sub>2</sub>CO<sub>3</sub>, which in turn is derived from the dissolving of soil CO<sub>2</sub>. The variation in soil PCO<sub>2</sub> produces an alkalinity variation of up to 15 meq L<sup>-1</sup> in stream water. Detecting and relating increases in alkalinity to decreases in stream SO<sub>4</sub> are significantly more difficult in the short term because of this effect. For example, modelled alkalinity recovery at Bear Brook due to a decline of 20 meq SO<sub>4</sub> L<sup>-1</sup> in soil solution is compensated by a decline from 0.4 to 0.2% for soil air PCO<sub>2</sub>. This compensation ability decays over time as base saturation declines. Variable PCO<sub>2</sub> has less effect in more acidic soils. Short-term decreases of PCO<sub>2</sub> below the long-term average value produce short-term decreases in alkalinity, whereas short-term increases in PCO<sub>2</sub> produce short-term alkalization. Trend analysis for detecting recovery of streams and lakes from acidification after reduced atmospheric emissions will require a longer monitoring period for statistical significance than previously appreciated.</p> <p style="line-height: 20px;"><b>Keywords:</b> CO<sub>2</sub> , alkalinity, acidification, recovery, soils, climate change