Detrital sediment in Florida's (USA) submerged cave systems may preserve records of regional climate and hydrologic variability. However, the basic sedimentology, mineralogy, stratigraphic variability and emplacement history of the successions in Florida's submerged caves remains poorly understood. Here we present stratigraphic, mineralogical, and elemental data on sediment cores from two phreatic cave systems in northwestern, Florida (USA), on the Dougherty Karst Plain: Hole in the Wall Cave (HITW) and Twin Cave. Water flowing through these cave represents subsurface flow in the Apalachicola River drainage basin, and the caves are located just downstream from Jackson Blue (1 st magnitude spring, >2.8 m 3 s −1 discharge). Sedimentation in these caves is dominated by three primary sedimentary styles: (i) ferromanganese deposits dominate the basal recovered stratigraphy, which pass into (ii) poorlysorted carbonate sediment, and finally into (iii) fine-grained organic matter (gyttja) deposits upsection. Resolving the emplacement history of the lower stratigraphic units was hampered by a lack of suitable material for radiocarbon dating, but the upper organic-rich deposits have a punctuated depositional history beginning in the earliest Holocene. For example, gyttja primarily accumulated in HITW and Twin Caves from ~5500 to 3500 cal yrs BP, which coincides with regional evidence for water-table rise of the Upper Floridian Aquifer associated with relative sea-level rise in the Gulf of Mexico, and evidence for invigorated drainage through the Apalachicola River drainage basin. Gyttja sediments were also deposited in one of the caves during the Bølling / Allerød climate oscillation. Biologically, these results indicate that some Floridian aquatic cave (stygobitic) ecosystems have been significantly devoid of recent organic matter supply in comparison to prehistoric intervals. The pre-Holocene poorly-sorted carbonate