Here we analyse geomorphic, pedologic and hydrologic processes of relevance to archaeological research on the pre-colonial irrigation system at Engaruka, Tanzania. Although archaeological studies have been carried out in Engaruka for several decades; geophysical processes have not been in focus, despite having the potential to contribute to the understanding of both the ancient irrigation system and the current land use in Engaruka. Geomorphology and pedology were explored through field surveys and mapping using air photos and satellite images. The effects of the flash-flood during the 1997-1998 El Nino were mapped and quantified in the field. Maximum flash-flood discharge in Engaruka River was estimated using Marming's Equation. The geomorphic study revealed that Engaruka is an environment where high-magnitude processes (debris flows, flash-floods, rock slides) dominate landform development. Low-magnitude processes (sheet-wash, wind erosion), transfer fine-textured sediment to low terrain, causing successive coarsening of soil texture in fields of the ancient irrigation system. Andisol occurrence in the dry environment is associated with current irrigation, indicating incremental improvement of arable land resulting from human land use. Andisols appear transient; discontinuation of irrigation has caused a reversion to Entisols, as water retention and structure deteriorate upon drying. A flash-flood during the 1997-1998 El Nino caused destruction of parts of the archaeological remains, with severe impact on current land use and settlements. Approximately 80 ha (4%) of the total area of the ancient remains were covered by debris flow deposits and alluvium, or scoured by new drainage lines of the water courses. The denudation caused by the single flash-flood is estimated to 9 mm in the catchment of Engaruka River. Manning's Equation yielded a least possible maximum discharge in Engaruka River, in the order of 270 m(3)/s, some 600-700 times higher than normal, dry season discharge.