The role of organic matter in soil boron (B) turnover and availability is not well understood. The forms and mobility of B are of special concern in soils irrigated with reclaimed wastewaters (RWW). We studied B distribution and binding in major components of two irrigated Mediterranean soils, with special emphasis on humus and water-mobile phases. The results showed that most B in the sandy loam Hamra soil and a large part in the clayey calcareous Grumosol was bound to extractable humus fractions and, in the Grumosol, to organic/mineral refractory residue, along with fractions of free (non-silicate) iron/aluminium (Fe/Al) minerals and aluminosilicates. Among humus fractions, the major B carriers were humin, Fe/Al-humates (complexed firmly, presumably through polyvalent Fe/Al cations), and calcium/magnesium (Ca/Mg)-humates (bridged to soil particles through divalent cations), and to a much lesser extent fulvic-Fe/Al (Hamra) and fulvic-Ca/Mg (Grumosol) complexes. The mode of B preferential binding indicates an origin of the soil humus from lignin of plant cell walls and membranes. In water extract, B was bound firmly (non-exchangeable) to coarse colloids >0.20 µm, presumably of organic/bacterial origin. Boron was not detected in the exchangeable fraction. This raises the question of the forms of bioavailable B in the soils. It can be assumed that the bulk of B in the soil–plant system circulates among plants (lignin) and the inherited soil organic matter/humified material. It is noteworthy that irrigation with RWW resulted in a slight increase of mannitol-extractable B and a redistribution of humus-B in favour of firmly bound Fe/Al-humate complexes.