Boating is a major vector for aquatic invasive species that cause significant economic and ecological impacts, necessitating biofouling control that goes beyond simply maintaining boat operations. However, new regulations restricting the use of antifouling paints-a common control tactic along with hull cleaning-have not considered the consequences to invasive species management. As a result, there is a critical need for a biofouling control strategy that both protects water quality and minimizes invasive species transport. We compared recruitment of fouling organisms to experimental plates (1) treated with hull coatings after 1 month and, for copper-based paint, after 1-, 3-, 6-, and 12-month submersion times; (2) after application of California's in-water hull cleaning practices; and (3) among locations within and between geographically separated harbors. Copper-based paint was initially effective at reducing fouling but lost effectiveness over time and was fouled heavily within 12 months. On plates with copper-based paint, nonnative species typically recruited first and facilitated the recruitment of other species. Nontoxic coatings were readily fouled, and invasive species (Watersipora subatra and Hydroides spp.) settled more often on ceramic epoxy and/or siliconized epoxy ("slick") coatings. Recruitment was higher in the harbor in the warmer water region. Depending on the harbor, W. subatra, Ciona spp., and Filograna implexa recruitment was correlated with water flow, the presence of conspecifics on the docks, or both factors. Strong seasonal recruitment was evident for Ciona spp., F. implexa, and Bugula neritina. Algae dominated the light-exposed surfaces of plates, and invertebrates dominated the shaded surfaces. California's hull cleaning practices did not stimulate fouling, which contradicted previous findings. Our findings informed the development of an integrated pest management framework for biofouling control on boat hulls that is adaptable to different regions and boater needs. This novel approach balances effective boat operations and protection of ecosystem health while simultaneously addressing water quality and invasive species transport.