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Polyelectrolyte multilayers are fabricated using the layer-by-layer (LbL) technique. The conditions used during and after their assembly allow the fine-tuning of multilayer properties such as surface charge, roughness, stiffness and wettability. Using this technique, thin films can be rationally designed for specific applications including antifouling, antireflection, antifogging, drug release, as well as creating self-cleaning surfaces and controlling cell growth behavior. The work in this dissertation focuses on understanding the fundamental mechanisms of PEMU growth and developing methods to control the thin film properties. Polyelectrolyte multilayers (PEMUs) growth has been described by two models: linear and exponential. In the linear growth mode, each added layer of polyelectrolytes compensates the charge on the surface. By comparison, exponentially growing systems allow the diffusion of at least one of the components of the multilayer into the entire film creating an excess of polymer charge that persists after build-up. This excess is compensated by small counterions that maintain the charge balance within the film. Although the ionic population within the PEMUs has been detected and quantified, the spatial distribution of the ions remains to be determined. As part of the work presented in this dissertation, we use a multilayer system that grows exponentially to determine the ionic content and the local distribution of counterions in polyelectrolyte thin films. In particular, multilayers of poly(diallyldimethylammonium) (PDADMA) and poly(styrenesulfonate) (PSS) were built on a stimuli-responsive substrate (aluminum) and subsequently released in alkaline solution to access the buried interface for further characterization. Elemental composition of the substrate/film and film/air interfaces were obtained using X-ray photoelectron spectroscopy. PDADMA/PSS thin films have a non-stoichiometric composition with an excess of positive polyelectrolytes within the bulk. Excess of PDADMA was detected on both sides of the free-standing PEMU confirming the diffusion of the positive polyelectrolyte species through the film all the way to the underlying substrate. The chemical composition and mechanical properties of these PEMUs were studied to obtain insights into the mechanism of build-up and the model describing the growth of the polyelectrolyte thin films. The ionic content was subsequently determined by exchanging the counterions left in the multilayer with radiolabeled ions. Finally, neutron reflectometry was used to probe the spatial distribution of the counterions that populate the PEMUs, revealing the internal structure of the films and a uniform distribution of the ionic population in bulk of the PEMUs. Using the same method for releasing PEMUs after assembly, we design Janus films consisting of PDADMA/ PSS multilayers with a final layer of perfluorinated Nafion polymer. Nafion capped films showed amphiphilic properties with a hydrophobic and a hydrophilic side. Nafion was allowed to diffuse throughout the film at high temperature creating a gradient of hydrophobicity within the bulk of the PEMU. The impact of temperature and salt concentration on the integrity and properties of polyelectrolyte multilayers was then investigated. Janus nanofilms were more resistant to dissolution at high salt concentrations compared to hydrophilic PDADMA/PSS multilayers. In a separate project, thin anionic and zwitterionic coatings were designed to repel algae from ion exchange resins. PSS and a copolymer of PSS and 3-[2-(acrylamido)-ethyldimethyl ammonio] propane sulfonate zwitterionic group (AEDAPS) (PSS75-co-AEDAPS25 and PSS50-co-AEDAPS50) were used to apply a thin polymeric coating on the surface of anion exchange resins. The deposition of the polyelectrolytes onto the resin particles was followed using UV-visible spectroscopy. After successful adsorption, PSS and PSScoAEDAPS polyelectrolyte coatings inhibited the settlement of Chlamydomonas reinhardtii algae onto the resin particles.