Bathroom-rich greywater coming directly in contact with virgin soil for years contaminates soil and alters its properties. The degree of alteration of soil properties may also depend on geological settings from which the soil was formed. The present study was designed to investigate the physico-chemical and geotechnical properties of greywater-contaminated soil (GCS) in different soils of basement complex formation. Soil samples were collected from greywater discharge zones and control soil (CS) in two locations (Mapo in Ibadan, Oyo State and Isolu in Abeokuta, Ogun State, Nigeria) at the depths of 0.5, 1.0 and 1.5 m from the surface, and the soil properties were analysed following standard procedures in the laboratory. The experiment consists of two modes: CS with no presence of greywater and GCS. The results of this study showed that alteration of most analysed properties depends greatly on sampling depth. There is increased in soil pH, cation exchange capacity, dry density (DD), saturated hydraulic conductivity (K sat) and shear strength (SS) in GCS at Mapo over their control values, while porosity, Atterberg limits (ALs), plasticity index and moisture content (MC) were reduced relative to the CS at all sampling depths. However, only bearing ratio improved at each sampling depth in GCS at Isolu, while alterations in other analysed properties did not follow clear trend. Correlation coefficient showed positive correlation between % clay and AL, porosity and ALs; MC and ALs at 1% level, while negative correlation exists between DD and ALs, % sand and ALs as well as K sat and ALs at the two locations. Two-way ANOVA showed that there is a significant difference at 5% level (p < 0.05) based on sampling depths for most analysed properties except SS, organic matter and soil resistivity. Further investigation is needed to study the trend of alteration of soil properties with depth on GCS at other soil types and geological formations.