Patterns of soil properties in highland environments remain poorly understood and limited knowledge exists on soil quality with respect to land use systems and topographic configurations. In this study, patterns of 12 surface soil physicochemical properties were assessed over a period of three years with respect to land use systems and toposequence positions in the Rwizi catchment of the Lake Victoria Basin. Four land use systems constituting mulched banana, unmulched banana, grassland and tree plantation, and three toposequence positions stratified as footslope, midslope and summit were considered and three replications were applied resulting in a total of 36 sites for soil properties measurements over a three-year period. Topographic attributes (elevation, slope gradient, slope aspect, and location) were collected at each site and correlated with surface soil properties. With the exception of pH and Ca, surface soil physicochemical properties are revealed to be optimal in the catchment. Greater spatial variation was found with soil chemical properties (8–57%) compared to physical properties (7–19%). Land use system registered significant effects (p < 0.05) for all soil chemical properties, as well as bulk density. Toposequence position is shown to have significant (p < 0.05) effects on soil pH, Soil Organic Matter, available P, N and soil texture. The effect of toposequence position revealed better soil quality along the catenary sequence summit > footslope > midslope. Strong and significant regression coefficients (r2 > 0.6, p < 0.05) for topographic attributes were found with soil pH, available P, K, Ca, Mg and sand. Overall, the land use system effect supersedes toposequence position in accounting for variations in surface soil physicochemical properties. Although environments of the Lake Victoria Basin are subject to intense agricultural activity and are usually assumed to be degraded, surface soil physicochemical properties in this part of the catchment reflect relatively healthy soil quality conditions.