For the first time, a crossflow electrochemical filtration system containing multiwalled carbon nanotubes (MWNTs) blended with buckypaper as a flat sheet dual membrane electrode was investigated for the removal of two contaminants of emerging concern, Ibuprofen and Bisphenol A. Breakthrough experiments revealed that a crossflow configuration could be highly efficient in eliminating both contaminants at applied DC potentials of 2 and 3 V over an extended period, from pure salt electrolyte as well as from synthetic secondary wastewater effluent. The shear flow provided consistent surface coverage resulting in excellent sorption performance. The long residence time of the two contaminants within the membrane (18.3 s) was sufficient enough to allow for almost complete degradation of phenolic aromatic products and quinoid rings and the resulting formation of aliphatic carboxylic acids, which was more evident at a higher applied potential (3 V). The formation of the non-toxic aliphatic carboxylic acids is a clear indication of the superior electrochemical performance of the crossflow mode over the dead-end flow-through system. Moreover, this study provides an in-depth understanding of different factors such as filter surface area and residence time that can greatly affect the removal of the contaminants considered.