There is an increasing interest in the use of Saccharina latissima (sugar kelp) as food, but the high iodine content in raw sugar kelp limits the daily recommended intake to relatively low levels. Processing strategies for iodine reduction are therefore needed. Boiling may reduce the iodine content effectively, but not predictably, since reductions from 38–94% have been reported. Thus, more information on which factors affect the reduction of iodine are needed. In this paper, sugar kelp cultivated at different depths were rinsed and boiled, to assess the effect of cultivation depth on the removal efficacy of potentially toxic elements (PTEs), especially iodine, cadmium, and arsenic, during processing. Raw kelp cultivated at 9 m contained significantly more iodine than kelp cultivated at 1 m, but the difference disappeared after processing. Furthermore, the content of cadmium and arsenic was not significantly affected by cultivation depth. The average reduction during rinsing and boiling was 85% for iodine and 43% for arsenic, but no significant amount of cadmium, lead, or mercury was removed. Cultivation depths determined the relative effect of processing on the iodine content, with a higher reduction for kelp cultivated at 9 m (87%) compared to 1 m (82%). When not taken into consideration, cultivation depth could mask small reductions in iodine content during rinsing or washing. Furthermore, since the final content of PTEs was not dependent on the cultivation depth, the type and extent of processing determines whether cultivation depth should be considered as a factor in cultivation infrastructure design and implementation, or alternatively, in product segmentation.