We report on a molecular fabrication approach to precisely control surface ζ potentials of polymeric thin layers constructed by electrostatic layer-by-layer (LbL) assembly methods. The protocol established allows us to achieve surface isoelectric points (IEP) in the pH range of 6–10. Poly(acrylic acid) (PAA, a weak polyanion) and poly(diallyldimethylammonium chloride) (PDADMAC, a strong polycation) were chosen to build up the bulk films. The weak polycation polyethylenimine (PEI) was applied as a top layer. A unique feature of this approach is that the chemical composition of the top layer is not affected by the manipulation of the ζ potential of the films. Surface charge tuning is achieved by controlling the degree of ionization of the weak polyelectrolytes at various pH values and subsequent manipulation of the amount of polyelectrolyte deposited in the penultimate and last layers, respectively. Following assembly and characterization, the films were used as candidates for antifouling surfaces. The fouling behavior of barnacle cyprids and bacteria on the LbL films with similar hydrophilicity and roughness but different surface charge densities were studied. We found that more cyprids of Amphibalanus amphitrite settled on the negatively charged LbL film compared to the neutral or positively charged LbL film. In bacterial adhesion tests employing Pseudomonas, Escherichia coli, and Staphylococcus aureus, more bacteria were observed on the positively charged LbL film compared with the neutral and negatively charged LbL films, possibly as a result of the negative potential of the bacterial cell wall. The procedures proposed allow one to adjust surface isoelectric points of LbL architectures to achieve optimal antifouling performance of a given material taking into account specific pH values of the environment and the character of the fouler.