The shallowness and poor quality of soils in Namibia is a reality, one which is hard to escape and costly to remedy. There are multiple reasons for these adverse conditions. The sparse plant growth and cover found in an arid climate means that very little plant litter returns to the soil as organic matter – to the detriment of soil fertility, microbial life and the physical properties of the soil. Organic matter mineralises rapidly in soils heated excessively by direct sun, while wind, overgrazing and the removal or burning of crop residues further limit the supply of organic matter to the soil.

Low rainfall makes for a dry soil regime with little chemical weathering of parent materials and thus low quantities of the clay minerals, which are needed to store and supply nutrients to plants. High evaporation rates can create an accumulation of salts in areas where there is moderate rainfall or surface flow.

The shallow Leptosols and stony Regosols offer limited soil volume in which water and nutrients can be stored or plants rooted. These soils are the result of a slow rate of weathering; water erosion from high-intensity rainfall events and high rates of runoff; and wind erosion of sparsely vegetated, desiccated soils.

The sandy Arenosols of eastern and northeastern Namibia hold little water or nutrients, as well as being somewhat acidic. Silty and fine sandy soils, such as those of northcentral and northeastern Namibia, are prone to capping and compaction. This interferes with aeration; water infiltration, percolation and storage; and nutrient uptake, root growth and biological activity. Thin crusts form on the surface when aggregates (called peds) of bare soil are broken down by the impact of raindrops and fine detached particles clog soil pores. Accumulations of silica and salts and the drying effects of sun and wind then harden these crusts. Soil aggregates are broken down and subsurface hardpans of low porosity and permeability form as a result of repeated pressure on the soil surface caused by heavy agricultural machinery or trampling by grazing animals.

The Solonchaks contain high levels of salts that are toxic to plants and cause them to become water stressed by hampering water uptake. The sodium-rich Solonetzes present physical problems for plant growth as a result of their hard crusts, poor infiltration and waterlogging. High concentrations of salts often develop in soils that are irrigated, especially in areas where evaporation rates are high, such as those at the Hardap Agricultural Scheme where salts from the water and fertilisers accumulate over time.

While Namibia's Calcisols do contain higher concentrations of nutrients, their uptake and use by plants is suppressed by an imbalance between nutrient bases such as calcium, potassium and magnesium.