Microfiltration (MF) membranes with chitosan/polystyrenesulfonate (CHI/PSS) functional layer coated surface can act as a barrier against emerging contaminants (ECs) in water under low pressure. One (one bilayer) or two functional layers are enough for the removal of lidocaine (LD, 100%) and ibuprofen (IBU, >75%). The effect of various ions, surfactant and humic acid is studied along with the influence of feed pH. Phosphate interferes negatively with the removal efficiency of membrane for IBU and sulfamethoxazole (SMZ). The reusability of the membranes are illustrated by the desorption studies of LD. The extended life of membrane and hence the antifouling nature of the selected ECs indicate its potential in small scale filtration units. Effect of ionic strength in feed and in deposition medium on the rejection percentage is presented. This study shows that various mechanisms depending on the properties of ECs are responsible for the rejection of ECs.