Perchlorate, a common aquatic contaminant, is well known to disrupt homeostasis of the hypothalamus-pituitary-thyroid axis. This study utilizes the threespine stickleback (Gasterosteus aculeatus) fish to determine if perchlorate exposure during certain windows of development has morphological effects on thyroid and gonads. Fish were moved from untreated water to perchlorate-contaminated water (30 and 100 mg/L) starting at 0, 3, 7, 14, 21, 42, 154 and 305 days post fertilization until approximately one year old. A reciprocal treatment (fish in contaminated water switched to untreated water) was conducted on the same schedule. Perchlorate exposure increased angiogenesis and follicle proliferation in thyroid tissue, delayed gonadal maturity, and skewed sex ratios towards males; effects depended on concentration and timing of exposure. This study demonstrates that perchlorate exposure beginning during the first 42 days of development has profound effects on stickleback reproductive and thyroid tissues, and by implication can impact population dynamics. Long-term exposure studies that assess contaminant effects at various stages of development provide novel information to characterize risk to aquatic organisms, to facilitate management of resources, and to determine sensitive developmental windows for further study of underlying mechanisms.