Despite its frequent use in terrestrial and freshwater systems, there is a lack of published experimental research examining the effectiveness of spray-delivered chemicals for the management of non-indigenous and/or unwanted pests in marine habitats. This study tested the efficacy of spraying acetic acid, hydrated lime and sodium hypochlorite for the control of marine fouling assemblages. The chemicals are considered relatively 'eco-friendly' due to their low toxicity and reduced environmental persistence compared to synthetic biocides, and they were effective in controlling a wide range of organisms. Pilot trials highlighted acetic acid as the most effective chemical at removing fouling cover, therefore it was selected for more comprehensive full-scale trials. A single spray of 5% acetic acid with an exposure time of 1 min effectively removed up to 55% of the invertebrate species present and 65% of the cover on fouled experimental plates, while one application of 10% acetic acid over 30 min removed up to 78% of species present and 95% of cover. Single-spray treatments of 5% acetic acid reduced cover of the tunicate pest species Didemnum vexillum by up to 100% depending on the exposure duration, while repeat-spraying ensured that even short exposure times (1 min) achieved approximately 99% mortality. Both 5 and 10% acetic acid solutions appeared equally effective at removing the majority of algal species. This technique could be used for controlling the introduction of unwanted species or preventing the spread of pests, and is applicable to use on a variety of natural and artificial substrata, or for the treatment of structures that can be removed from the water.