An understanding of the soil moisture variability is indispensable to characterize the relation between a region’s hydrology, ecology and hydropedology. The objectives of the present study were: (a) to understand spatio-temporal variability of soil moisture content under different land covers in the humid tropical Brahmaputra basin and (b) to characterize the differences in spatial and temporal patterns of soil moisture content and surface and subsurface runoff generation patterns influenced by different classes of landuse and land cover by application of the SWAP agrohydrological model. An experimental study site located in Amingaon, Kamrup district of Assam, India was selected for monitoring of profile averaged soil moisture. Four plots composed of homogenous land covers of broadleaved deciduous forest, shrubs and bamboo were selected with soil moisture monitoring facility. Hydrometeorological data mainly daily rainfall, maximum temperature, minimum temperature, relative humidity, solar radiation, wind-speed were monitored for two years from January 2011 to December, 2012. The SWAP model was calibrated from profile probe measurements for May 2011 to October 2011. The model simulations revealed that land use and land covers significantly influenced the moisture contents, surface and subsurface runoff .Undisturbed forest soils, having high degree of macroporosity, showed higher preferential flow and low runoff. However, paddy fields exhibited very high surface runoff due to lower infiltration owing to hard pan formation at a shallow depth. The subsurface drainage and soil moisture storage was moderate in paddy. Soils under Jhum cultivation showed significant numbers of active macropore in the upper soil layer, whereas the macropore connectivity was apparently lost in the lower horizons. Therefore surface runoff was very high. The subsurface drainage as well as the soil moisure storage was higher in jhum. In case of grasslands the higher unsaturated hydraulic conductivity favoured more infiltration of water causing higher subsurface flow and soil moisture storage. Less infiltration of rain water was observed in grasslands, where the surface initiated macropores were blocked by eroded fine soil particles causing higher surface runoff. In case of bamboo, the subsurface drainage as well as the soil moisture storage was high indicating higher preferential flow in the lower soil layers. The broadleaved deciduous forest soil thus generated high magnitudes of surface runoff due to its clayey soil. The subsurface drainage was high but the soil moisture storage was moderate. In tea-garden, surface runoff rate from the tea garden was moderately high. The subsurface drainage and soil moisture was also moderately high in forest under Jhum due to lower saturated hydraulic conductivity. In case of bamboo, the subsurface drainage as well as the soil moisture storage was high indicating higher preferential flow in the lower soil layers. The broadleaved deciduous forest soil thus generated high magnitudes of surface runoff. The subsurface drainage was high but the soil moisture storage was moderate. In case of shrubs and alpine shrubs, due to well developed macropore network, more percolation of water resulted in lesser surface runoff. The subsurface drainage and soil moisture was also moderately high. In case of needleleaved evergreen forest, subsurface flow was less and soil moisture storage was moderate. In case of broadleaved evergreen forest subsurface flow was very high but soil moisture storage was less. In case of croplands and plantation, obstructed macropore connectivity resulted in higher runoff. In case, of plantation, the subsurface drainage was high but soil moisture storage was moderate. In case of cropland, subsurface drainage was moderate but soil moisture storage was high.