Surface water pollution is a challenge due to effluent discharge from land-based factors like agro-based sectors, settlements, and poor sanitation. The research investigated the spatial and seasonal variation of physico-chemical and biological water quality due to land use changes along the Thika River sub-catchment, Upper Tana, Kenya. The study applied purposive sampling technique from the different zones within the catchment during the dry and wet season of 2021. The samples were tested for physico-chemical and microbial contaminants. R-studio was used to calculate the mean values and t-test performed at a 95% confidence interval to determine variation of the parameters in the two seasons and mean levels compared to the Kenya Bureau of Standards (KEBS) 2010 and the World Health Organization (WHO) acceptable quality for drinking water. There was significant variation in sulphate and nitrate concentration, total coliform and fecal coliform and no significant variations in physical parameters throughout the seasons. The total coliform and fecal coliform exceeded KEBS and WHO limits.