Biogenic volatile organic compounds (BVOCs) are important molecules that may act as indicators for aquatic ecosystem health, functioning and composition. However, aquatic BVOC sampling methods are currently restricted to ex situ settings, which means that the volatiles identified and quantified may not strictly represent those produced in situ. Here we developed and deployed a novel chamber, the ‘BlueVOC’, enabling the capture of BVOCs from benthic organisms in situ for the first time. Using a preliminary design (BlueVOC 1.0), we sampled the sum volatile metabolites – or, the volatilome – from a scleractinian coral (Montipora cf. digitata), an alcyonacean coral (Cladiella sp.), and a macroalgae (Halimeda sp.) on a coral reef flat. Despite the taxonomic diversity of incubated species, 48% of BVOCs detected from targeted organisms were shared between taxa, and 99.1% were also detected from water and sediment samples, suggesting that BVOC emissions from target organisms were obscured by the background BVOCs from the environment. To better capture BVOCs emitted by the targeted benthic organisms, we revised our BlueVOC design, sampling procedure and analytical methodologies. We applied these modifications to profile the volatilome from a key coastal mangrove, Avicennia marina, targeting aerial roots (pneumatophores) under contrasting tidal phases. Our data from BlueVOC 2.0 confirmed an improved capture of BVOCs emitted by the target organisms compared to environmental signals, yielding over twice as many organism-derived BVOCs – with 19% being shared between tidal states. We highlight the importance of effective identification of target organism-produced BVOCs from the chemically complex marine environment and demonstrate that our BlueVOC 2.0 methodology enables capture of the volatilome from aquatic organisms in their native states.