The study was designed to investigate the dynamics of the goitrogen-iodine balance in Igbokoda brackish and Ogbese fresh water bodies in Ondo State, Nigeria. The parameters determined include iodine, thiocyanate, chloride, nitrate, calcium, magnesium hardness, calcium hardness, total hardness, and total coliform counts in water, sediment and/or fish (flesh and serum). The fish were subjected to a number of treatments (boiling with water or sodium chloride solution, frying or roasting) prior to analysis. The iodine level (microg I/100g) in the flesh of fish varied with size, treatment and location; it increased with size, was reduced by some treatments (boiling with either water or NaCl solution), while frying and roasting did not affect the level. The least values were 93.45 (Ogbese fish boiled with NaCl solution) and 160.94 (Igbokoda fish boiled with either water or NaCl solution). On the whole, Igbokoda (160.94-314.08) had higher values than Ogbese (93.45-205.06). Serum iodine (microg I/100mL) was equally higher in Igbokoda (5.00-9.00) compared to Ogbese (2.80-5.00). Only the large sized fish of Ogbese recorded a value of 5.00 micromol/L for thiocyanate while this parameter was not detected in other samples. The calculated I/goitrogen ratios (I/Ca, I/NO3, I/Cl and I/SCN) were higher for Igbokoda water than Ogbese water with the exception of I/Mg. This was equally reinforced by the total count of coliforms (goitrogenic), which was higher in Ogbese (3.0 x 10(3)) than in Igbokoda (2.7 x 10(3)). These results indicate that the Igbokoda brackish water body would be a better source of iodine than Ogbese fresh water body for the population dependent on them.