In this paper, a filter probe integrated into a computerized pneumatic sampler for capillary electroseparations was developed for an on-line monitoring of bioprocesses. The optimization of the performance of the coupled system was done by using a response surface modeling and three-level two-factor design. The resolution was found to be the most important parameter influencing the performance of an on-line analysis of the microbial metabolism. For the on-line analysis the migration time and detection limit were also found to be important parameters. Different parameters were combined by using an overall desirability function to find optimum conditions for all parameters. The equipment with an optimized separation protocol was used to monitor the bioaccumulation of Cu, Zn, Co and Cd (with detection limits 0.46, 0.37, 1.2, 0.84 mM correspondingly) by the Rhodococcus sp. bacteria isolated from the highly polluted technogenic soil of northeastern Estonia during a 2-week experiment.