Abstract On the east coast of South Andros Island, Bahamas, a major bank–marginal fracture system characterised by vertically extensive cavern systems (blue holes) is developed sub-parallel to the steep-sided deep-water re-entrant of the Tongue of the Ocean. In addition to providing a discharge route for meteoric, mixed and geochemically evolved saline groundwaters, a strong local circulation occurs along the fracture system. This generates enhanced vertical mixing within voids of the fracture system, evidenced by the increasing mixing zone thickness, and the thinning and increasing salinity of brackish lens waters from north to south along the fracture system. Furthermore, tidally driven pumping of groundwaters occurs between the fracture and adjacent carbonate aquifer affecting a zone up to 200 m either side of the fracture. The resultant mixing of groundwaters of contrasting salinity and P CO 2 within and along the fracture system and with the surrounding aquifer waters, together with bacterial oxidation of organic matter, generates significant potential for locally enhanced diagenesis. Undersaturation with respect to calcite within the fresh (or brackish)–salt water mixing zone is observed in the fracture system and predicted in the adjacent aquifer, while mixing between the brackish fracture lens and surrounding high P CO 2 fresh waters causes dissolution of aragonite but not calcite. The latter gives rise to considerable secondary porosity development, because active tidal pumping ensures continued renewal of dissolutional potential. This is evidenced by calcium and strontium enrichment in the brackish lens which indicates porosity generation by aragonite dissolution at a maximum rate of 0.35% ka −1, up to twice the average estimated for the fresh water lens. In contrast saline groundwaters are depleted in calcium relative to open ocean waters suggesting the formation of calcite cements. The development of a major laterally continuous cavernous fracture zone along the margin of the carbonate platform permits enhanced groundwater flow and mixing which may result in generation of a diagenetic `halo' at a scale larger than that generally recognised around syn-sedimentary fractures in fossil carbonates. This may be characterised by increased secondary porosity where a relative fall in sea-level results in exposure and formation of a meteoric groundwater system, or cementation by `marine' calcite both below this meteoric system, and where the bank surface is flooded by seawater.