A late Pleistocene to Holocene submerged and encrusted speleothem exhibits a complex history including a meteoric phase and two marine phases. A combined study using petrography, mineralogy, and inorganic and organic geochemistry, as well as geochronology has shown that phototrophic and heterotrophic biological activity impacted carbonate precipitation during all phases of carbonate accretion. The stalactite formed ca. 30 m below modern sea level at a marginal overhang in the Blue Hole of Lighthouse Reef Atoll. Unlike purely meteoric speleothems, the Belize example consists of a meteoric core, a marine aragonite crust, and a serpulid-micrite-rich outer crust as a result of postglacial flooding of the karst cave. The core of the stalactite has a tufaceous texture, containing algal or microbial remains, and consists entirely of low-magnesium calcite, formed 19.55–10.68 kyr BP. The texture suggests that the stalactite formed at the cave entrance, and, hence, the former cave ceiling had apparently collapsed earlier during the Pleistocene. Oxygen (δ18O) and carbon (δ13C) isotopes across the core suggest a trend towards drier conditions and reduced soil and plant cover after the last glacial maximum. The marine aragonite crust consists of stacked botryoids in which individual crystals up to 700 μm have dark terminations enriched in high-magnesium calcite. This crust accreted from 10.82 to 9.95 kyr BP in warm shallow water during the early Holocene thermal optimum. Carbonate accretion rates were considerable and averaged 125 μm/yr. The crust has a dense, laminated texture on one side and a porous, shrubby texture on the other. The presence of n-C16:1ω5, n-C17:1ω6, and 10Me-C16 fatty acids in the laminated crust suggests that sulfate-reducing bacteria contributed to aragonite formation in an environment that was less open than the formation environment of the porous crust, where these biomarkers are lacking (n-C16:1ω5, n-C17:1ω6) or are less abundant (10Me-C16). Enrichment of 34S and 18O in carbonate-associated sulfate (CAS) relative to seawater sulfate also suggests sulfate reduction during carbonate formation. The greater contribution of heterotrophic processes to aragonite precipitation in the laminated crust is also reflected in δ13C values as low as −1.3‰, whereas no such depletion is observed in the aragonite of the porous crust (δ13C values as low as 0.0‰). A pronounced isotopic variability and excursions to positive δ13C values as high as +3.5‰ in the inner half of the laminated crust indicate an episodic, local impact of photosynthesis on aragonite precipitation, whereas the lack of such excursions in the porous crust (δ13C values as high as +1.5‰) is again best explained by a more open environment of formation. After a ca. 5 kyr hiatus, from 4.39 kyr BP, a biogenic crust of abundant serpulids and finely crystalline, microbial and detrital carbonate, consisting of high-magnesium calcite and aragonite, accreted on the outer surface of the stalactite. Outermost crust accretion was probably influenced by the inundation of the Lighthouse Reef lagoon that started to shed abundant fine-grained carbonate sediment into the Blue Hole. The stalactite broke off the cave ceiling either before or after the formation of the outermost crust, likely due to seismic movements along the nearby plate boundary. The study demonstrates that like speleothems from the terrestrial realm, submerged stalactites may have had complex histories with great potential as paleoenvironmental archives.