Ancient terraced fields in ephemeral stream valleys in the Negev desert enabled farming based on runoff water from local rainfall. The runoff was captured by stone terrace walls, which were built across suitable wadis in various archaeological periods. Runoff floods added not only water to the fields but also fine sediment. However, alluvial stratification is usually absent in such terraced wadi fields. Why? We addressed this question at the rural archaeological site of Horvat Haluqim in the central Negev highlands. Our geoarchaeological excavations in Area 3 of Terraced Field 12 revealed the existence of laminar alluvial stratification, but only in the upper 5 cm. Micromorphology showed a gradual decline in the preservation of laminae with depth. Radiocarbon dating showed that the upper 50 cm of the terrace soil accumulated during the past 1300 years. Therefore, the average aggradation rate seems about 0.4 mm/year, similar to modern sedimentation measurements. We found evidence for bioturbation, particularly by ants and scorpions, in the terraced wadi fields at Horvat Haluqim. Scorpions evict the soil crumbs, excavated from the subsoil, on one side of the crescent-shaped entrance to their burrows. Ants, on the other hand, place the excavated soil crumbs all around the entrance to their underground nest. Besides bioturbation, human soil disturbance by farming is far more destructive to alluvial stratification. Hoeing and ploughing (tillage) can erase alluvial laminae from the surface to a depth of about 10 cm in one farming season. Clear evidence of ancient farming activities in Area 3 was found in darker soil layers from a depth of 45 cm–92 cm. Laminar alluvial strata have not survived in these layers. Micromorphology revealed fine charcoal, bone and pottery fragments, interpreted as kitchen/household refuse added as fertilizer to the aggrading soil surface. In addition, non-burned dung fragments and non-charred spherulites were found, indicating also the use of animal dung as manure. Darker soil layers have a lower bulk density and a high porosity with an extremely large amount of fine pores, probably ancient root channels of barley or wheat. Though runoff flows kept adding laminated alluvial layers to the aggrading terraced wadi fields, the fine laminae (initial facies) did not endure the tooth of time. They were gradually obliterated by bioturbation and/or rapidly erased by human farming activities (tillage and manuring), so that laminae are non-existent in the ultimate facies of the aggrading sediment-soil in agricultural terraced wadi fields.