Proper membrane process design can be a difficult task to accomplish when fouling is present, and must be faced. Engineers usually consider the project variables concerning productivity and selectivity and follow these targets. However, in the presence of fouling, additional parameters must be considered, implying better knowledge of fouling phenomena. One possible solution to increase the reliability of a process is the use of stable control systems. This article reports a suitable method to reach this target, based on the boundary flux theory. The knowledge of the boundary flux values permits avoidance of high fouling operating conditions on a selected membrane. The goal here was to determine the framework for control of an ultrafiltration (UF) and nanofiltration (NF) batch membranes-in-series process treatment for olive mill wastewater, relying on these boundary flux points, which will thereafter serve for the automatic control of the process by an advanced control system. In this work, boundary flux values equal to 10 Lh−1m−2 for the UF membrane module and 14.3 Lh−1m−2 for the NF one were estimated. Moreover, the membrane constant permeability loss, measured by integrating the sub-boundary fouling index, was estimated to be reduced in the order of 65.4% for the NF membrane after the applied pretreatment and UF. This strategy permitted attaining stable and constant productivity for both membranes. Moreover, it is shown that, relying on the boundary flux modelization, both types of control systems (feed control and pressure control) could be used reliably. The proposed approach could help safely narrow the overdesign of membrane processes due to fouling issues and thus would have an impact on the reduction of the costs for both membrane processes.