Overfertilization in farmland-to-orchard conversion is causing severe deep soil acidification on the Loess Plateau, China. Although fertilizer nitrogen is the primary factor causing acidification, little is known about the contributions of other soil nutrients. Here, we investigated the vertical distributions of pH and available nutrients in deep soil profiles in croplands and rainfed and flood-irrigated apple orchards of different ages. Depth-averaged pH decreased by 0.25 units in 25-yr rainfed orchards and by 0.29 units in 30-yr irrigated orchards, although pH increased linearly with depth in all systems. However, compared with pH absolute values, differences in the relations between changes in soil pH (Delta pH, difference from "control" cropland) and depth suggested that changes in cropland soil pH might mask the responses of soil pH in orchards. The relations between soil pH and available nutrients differed substantially from those between Delta pH and Delta available nutrients. Nonsignificant relations between Delta pH and Delta NO3--N in 8-yr rainfed orchards and 10-yr irrigated orchards indicated that the changes in rather than the absolute values of soil NO3--N accounted for deep soil acidification. Partial least squares path models indicated that deep soil acidification was primarily associated with Delta NO3--N, Delta AP, Delta AK, and Delta Ex-Ca, compared with absolute values. The contributions of Delta available nutrients to Delta pH were typically dependent on irrigation, land-use types, and soil depths. Our study demonstrates that changes in available nutrients are better indicators than their absolute values of soil acidification in Chinese apple production systems.