"Click" chemistry-enabled layer-by-layer (LBL) deposition of multilayer functional polymer coatings provides an alternative approach to combating biofouling. Fouling-resistant azido-functionalized poly(ethylene glycol) methyl ether methacrylate-based polymer chains (azido-poly-(PEGMA)) and antimicrobial alkynyl-functionalized 2-(methacryloyloxy)ethyl trimethyl ammonium chloride-based polymer chains (alkynyl-poly(META)) were click-assembled layer-by-layer via alkyne-azide 1,3-dipolar cycloaddition. The polymer multilayer coatings are resistant to bacterial adhesion and are bactericidal to marine Gram-negative Pseudomonas sp. NCIMB 2021 bacteria. Settlement of barnacle (Amphibalanus (=Balanus) amphitrite) cyprids is greatly reduced on the multilayer polymer-functionalized substrates. As the number of the polymer layers increases, efficacy against bacterial fouling and settlement of barnacle cyprids increases. The LBL-functionalized surfaces exhibit low toxicity toward the barnacle cyprids and are stable upon prolonged exposure to seawater. LBL click deposition is thus an effective and potentially environmentally benign way to prepare antifouling coatings.