A perchlorate is a chemical compound containing the perchlorate ion, ClO4-. On Mars they are part of the soil, mostly in calcium salts.
Perchlorates in the Martian soil have been identified as a significant hazard to a martian settlement plan. Perchlorate was detected in martian soil at the level of ~0.6% by weight. It is conjectured to exist as a mixture of 60% Ca(ClO4)2 and 40% Mg(ClO4)2
In large amounts perchlorate interferes with iodine uptake into the thyroid gland. Because it is neither stored nor metabolized, the effects of perchlorate on the thyroid gland are reversible, though effects on brain development from lack of thyroid hormone in fetuses, newborns, and children are not. Perchlorate dust affects lung tissue.
Perchlorates are readily soluble in water and can be removed from surfaces by rinsing with water. Removing perchlorate from the settlement water supply can be done in a number of ways. Methods to remove perchlorates from water include reverse osmosis membranes, TSSE, biological remediation or photochemically via UV light on a metallic iron catalyst. Some bacteria will consume perchlorates, and as an added bonus, release oxygen.
Reducing dust intake into the settlement is a good objective. Washing vehicles, spacesuits and tool with water would reduce the intake at the source. Using suitports to enter EVA suits would also reduce perchlorate ingress into the settlement.