Soil samples were collected from six locations representative of the Nyando River catchment area of the Lake Victoria over a period of two years. Sampling was done four times in the year in February, May, September and December 2005 and 2006 in farms where maize, tea, sugar cane, coffee, rice and vegetables have been grown over the years. This coincided with the effects of different seasons and farming activities on residue levels of the pesticides in use. The objective was to investigate levels and distribution of organochlorine pesticides that have either been banned or are restricted for use in Kenya. Organochlorine pesticides investigated were DDT, lindane, aldrin, dieldrin, heptachlor, endrin, endosulfan (both α- and β- isomers and endosulfan sulphate), the sum is called “total” or Σendosulfan and methoxychlor. Prior to the ban or restriction in use, these pesticides had found wide applications in public health for control of disease vectors and in agriculture for control of crop pests. The analysis revealed presence of all the targeted pesticides with the highest mean concentrations for methoxychlor 138.97±1.517 μg/kg, Σendosulfan (30.267±2.098μg/kg), aldrin (18.317±0.276 μg/kg), respectively. The results show the presence of these pesticides in soils in the basin and this could be impacting negatively on the ecosystem health of the area.