The hydraulic conductivity (
K) of peat beneath the water table varies over short (annual) periods. Biogenic gas bubbles block pores and reduce K, and seasonal changes in the water table position cause peat deformation, altering peat pore size distribution. Although it has been hypothesized that both processes reduce Kduring warm dry summer conditions, temporal variations in Kunder field conditions have been explained previously by peat volume changes (strain) alone. We determine the effect of both controls on Kby monitoring changes in gas content (Δ γ), strain and Kwithin a poor fen. Over the growing season, Kdecreased by an order of magnitude. In the near‐surface peat (0.3–0.7 m), this reduction is more strongly correlated with Δ γ, providing the first field‐based evidence that biogenic gas bubbles reduce K. In the deeper peat (0.7–1.3 m), Kis correlated principally with strain. However, causality is uncertain because of multicollinearity between strain and Δ γ. To mitigate for multicollinearity, we took advantage of a peatland drainage experiment where the water table was artificially dropped at the beginning of the growing season, reducing correlations between strain and Δ γ. Δ γremained the primary cause of Kvariations just beneath the water table at a depth of 0.5–0.7 m, although further down through the peat profile (0.7–1.2 m) changes in Kwere controlled by strain. We suggest that the larger pore structure of the poorly decomposed peat just below the water table is impacted less by volume changes than that of the more decomposed peat at depth. However, within this poorly decomposed peat, Kis reduced by the high gas contents that result from higher rates of methane production. Copyright © 2012 John Wiley & Sons, Ltd.