Iodine is deficient in diets worldwide, leading to a range of undesirable health affects at the population level. Dairy products are a primary source of iodine in the diets for those populations in which iodised salt is not systematically utilised or available. Yet, the flows of iodine through dairy agroecosystems are not well understood. The aim of this research was to investigate iodine flows though the dairy agroecosystem; including the influence of atmospheric depositional inputs, environmental variables, season, husbandry and diet. Three farm based sampling campaigns were conducted in this investigation with milk, soil, silage, grass and feed iodine determined by inductively coupled plasma-mass spectroscopy, and non-parametric statistical analysis tests were conducted on data sets obtained. Natural iodine inputs into the environment are dominated by atmospheric deposition, which was dominated by sea spray, and thus location of farms to coast and prevailing wind direction. Herbage, and silage produced from herbage, strongly correlated with soil iodine, yet there was a strong disconnect between soil, forage and feed and the milk that results. This was due to the levels of iodine in supplemental feeds being ~10-fold higher than in forage derived feeds. The practice of feed supplementation, accentuated by summer housing of cows, led to elevated milk iodine.