Surface sediment geochemistry data comprised of:1) trace metals; 2) Pb isotope ratios; 3) organic pollutants (pharmaceuticals, hydrocarbons and organochlorines and microtox bioassay). Sediments were collected from sites situated along Nairobi, Mathare and Ngong Rivers, Nairobi, Kenya on January 16th, 2020. This data is published in the following research paper which should be cited; Vane, C.H., Kim, A.W., Lopes dos Santos, R.A., Gill, J.C., Moss-Hayes, V., Mulu, J.K., Mackie, J.R., Ferreira, A.M.P.J., Chenery, S.R. and Olaka, L.A., 2022. Impact of organic pollutants from urban slum informal settlements on sustainable development goals and river sediment quality, Nairobi, Kenya, Africa. Applied Geochemistry, 146: 105468. https://doi.org/10.1016/j.apgeochem.2022.105468