Evaluation of microbial loads and physico-chemicals of cassava mill effluent simulated soil was carried out using standard microbiological and biochemical techniques. This was to determine the effect of cassava mill effluent (CME) on rhizosphere microbial loads, physicochemical properties, nitrogenous salt and heavy metals. The results showed that CME effect on the physicochemical determinants (pH, Ca, Mg, K) and heavy metal determinant (Fe, Zn, Co, Ni, Pb and Mn) was concentration dependents. The nitrogenous salts (NO3, NH4+ and NO2) levels progressively increased with no significant differences (p>0.05 ANOVA). The microbial isolates were: Saccharomyces sp, Mucorindicus, Fusarium sp and Gliocladium sp for the fungal group. The bacterial group were Chromobacterium sp, Corynebacterium sp, Bacillus sp, Acinetobacter sp and Escherichia coli while the nitrogen-fixing bacterial group were Azotobacter sp., Azospirillum sp., Frankia sp., Bradyrhizobium sp., Hebaspirillum sp., Cyanobacteria (or blue green algae), Anabaena sp, Nostoc sp., Clostridium sp. and Rhizobium sp. There was no significant differences (p>0.05) in the rhizosphere microbial load across the concentration gradient at the CME-simulated plot phyto-remediated by Centrosema pubesscens and Calopogonium mucunoides. Agricultural wastes such as cassava mill effluent should be properly treated before discharging to the environment in other to prevent the loss of nitrogen-fixing bacteria and total heterotrophic bacterial genera that could be of immense importance to man.