Despite iodine being one of the most abundant of the minor elements in oxic seawater, the principal processes controlling its interconversion from iodate to iodide and vice versa, are still either elusive or largely unknown. The two major hypotheses for iodate reduction involve either phytoplankton growth in primary production, or bacteria during regeneration. An earlier study intended to exploit the unusual nature of anchialine environments revealed that iodide is oxidised to iodate in the bottom of such caves, whereas reduction of iodate occurs in the shallower parts of the water column. This investigation was made on the hypothesis that study of the nitrogen and phosphorus nutrient systems within the caves might offer a bridge between the iodine chemistry and the marine bacteria which are assumed to be the agent of change of the iodine in the caves. Accordingly, the hydrography, the nutrient chemistry, and some further iodine studies were made of two anchialine caves on the east coast of the Adriatic Sea in Croatia. Iodate and iodide were determined by differential pulse voltammetry and cathodic stripping square-wave voltammetry, respectively. Total iodine was determined indirectly, as iodate, after oxidation of reduced iodine species with UV irradiation and strong chemical oxidants. Nutrient concentrations were measured by spectrophotometry. Nutrient profiles within the well stratified water columns indicate a relatively short-lived surface source of nitrate and phosphate to the caves, with a more conventional, mid-water, nutrient regeneration system. The latter involves nitrite and ammonium at the bottom of the halocline, suggestive of both autotrophic and heterotrophic microbial activity. High iodate/low iodide deep water, and conservative behaviour of total inorganic iodine were confirmed in both systems. Iodate is reduced to iodide in the hypoxic region where nutrient regeneration occurs. The concentrations of organic iodine were surprisingly high in both systems, generally increasing toward the surface, where it comprised almost 80% of total iodine. As with alkalinity and silica, the results suggest that this refractive iodine component is liberated during dissolution of the surrounding karst rock. A major, natural flushing of one of the caves with fresh water was confirmed, showing that the cave systems offer the opportunity to re-start investigations periodically.