The effects of two types of organic matter (OM) (humic acid and protein) on colloid transport in porous media were investigated with column experiments and numerical modeling. Colloid deposition was explored in double-pulse experiments (DPEs) by injecting a pulse of OM to allow its pre-adsorption to iron-oxide-coated sand, followed by a pulse of latex microspheres. These experiments were compared with single-pulse experiments (SPEs), where one mixed pulse of OM and microspheres was introduced to the column. The experimental results show that pre-adsorbed and co-depositing OM may, respectively, limit initial and transient colloid deposition. The DPE results can be interpreted with an existing colloid transport model (random sequential adsorption: RSA). SPE results were interpreted with an extended RSA model (RSAE) that couples the process of OM co-deposition and blocking to colloid transport by introducing a conversion factor (K-conv) that reflects the blocking efficiency of OM. The calculations with the verified model suggest a comparable site blocking capacity of pre-adsorbed and co-depositing OM with a blocking capacity that differs for different sources of OM. Traditionally described as a modification of the chemistry of the overall deposition surface for the suspended particles, OM adsorption can also be interpreted as blocking local colloid attachment sites by the OM. This second interpretation may be more useful in describing nanoparticle deposition where the particle size is comparable to the length scale where a molecule of OM modifies the deposition surface.