| Rank | City | 2000 Population | Growth Rate (Annual) |
|---|---|---|---|
| 1 | Sioux Falls | 125,598 | 2.2% |
| 2 | Rapid City | 60,054 | 0.9% |
| 3 | Aberdeen | 25,183 | -0.1% |
| 4 | Watertown | 20,265 | 1.3% |
| 5 | Brookings | 18,825 | 1.4% |
| 6 | Mitchell | 14,608 | 0.6% |
| 7 | Pierre | 13,883 | 0.7% |
| 8 | Yankton | 13,504 | 0.9% |
| 9 | Huron | 11,865 | -0.7% |
| 10 | Vermillion | 10,249 | 0.2% |
| 11 | Spearfish | 8,678 | 1.9% |
| 12 | Madison | 6,523 | 0.2% |
| 13 | Sturgis | 6,474 | 0.6% |
| 14 | Brandon | 5,810 | 4.9% |
| 15 | Belle Fourche | 4,815 | 0.7% |
| 16 | Hot Springs | 4,146 | -0.6% |
| 17 | Milbank | 3,632 | -0.8% |
| 18 | Mobridge | 3,549 | -0.6% |
| 19 | Box Elder | 3,428 | 2.5% |
| 20 | Canton | 3,140 | 1.0% |
| 21 | Winner | 3,120 | -0.8% |
| 22 | Lead | 3,022 | -2.3% |
| 23 | Dell Rapids | 2,995 | 1.8% |
| 24 | Sisseton | 2,544 | 1.4% |
| 25 | Redfield | 2,524 | -1.0% |
| 26 | Flandreau | 2,372 | 0.3% |
| 27 | Chamberlain | 2,346 | -0.2% |
| 28 | North Sioux City | 2,288 | 1.2% |
| 29 | Lennox | 2,054 | 1.5% |
| 30 | Fort Pierre | 2,042 | 0.9% |
| 31 | Beresford | 2,003 | 0.8% |
| 32 | Custer | 1,971 | 0.9% |
| 33 | Webster | 1,943 | -0.7% |
| 34 | Hartford | 1,887 | 3.9% |
| 35 | Tea | 1,792 | 8.4% |
| 36 | Elk Point | 1,717 | 1.9% |
| 37 | Parkston | 1,668 | 0.6% |
| 38 | Wagner | 1,609 | 1.0% |
| 39 | Springfield | 1,562 | 6.4% |
| 40 | Miller | 1,533 | -0.9% |
| 41 | Volga | 1,457 | 1.0% |
| 42 | Gregory | 1,393 | -0.8% |
| 43 | Salem | 1,391 | 0.6% |
| 44 | Lemmon | 1,390 | -1.6% |
| 45 | Deadwood | 1,374 | -2.6% |
| 46 | Platte | 1,363 | 0.4% |
| 47 | Groton | 1,353 | 1.2% |
| 48 | Gettysburg | 1,334 | -1.2% |
| 49 | Clear Lake | 1,331 | 0.7% |
| 50 | Britton | 1,325 | -0.3% |
| 51 | Freeman | 1,314 | -0.3% |
| 52 | Clark | 1,277 | -0.1% |
| 53 | Tyndall | 1,236 | 0.3% |
| 54 | De Smet | 1,204 | 0.1% |
| 55 | Garretson | 1,168 | 2.4% |
| 56 | Eureka | 1,101 | -0.8% |
| 57 | Martin | 1,077 | -0.8% |
| 58 | Howard | 1,070 | -0.8% |
| 59 | Parker | 1,044 | 0.5% |
| 60 | Wessington Springs | 1,003 | -0.8% |
| 61 | Arlington | 993 | 0.8% |
| 62 | Harrisburg | 986 | 3.0% |
| 63 | Ipswich | 941 | -0.5% |
| 64 | Eagle Butte | 911 | 6.4% |
| 65 | Centerville | 908 | 0.3% |
| 66 | Mission | 906 | 2.2% |
| 67 | Marion | 891 | 0.7% |
| 68 | Scotland | 888 | -0.9% |
| 69 | Alcester | 879 | 0.4% |
| 70 | Philip | 877 | -2.0% |
| 71 | Crooks | 867 | 2.7% |
| 72 | Edgemont | 859 | -0.6% |
| 73 | Highmore | 847 | 0.1% |
| 74 | Whitewood | 844 | -0.5% |
| 75 | Viborg | 834 | 0.9% |
| 76 | Baltic | 823 | 2.1% |
| 77 | Wall | 818 | -0.2% |
| 78 | Lake Andes | 817 | -0.4% |
| 79 | Valley Springs | 795 | 0.7% |
| 80 | Hill City | 783 | 1.1% |
| 81 | Faulkton | 781 | -0.4% |
| 82 | Armour | 777 | -1.0% |
| 83 | McLaughlin | 767 | -0.2% |
| 84 | Kimball | 742 | -0.0% |
| 85 | Lake Preston | 737 | 0.9% |
| 86 | Onida | 735 | -0.4% |
| 87 | Selby | 733 | 0.4% |
| 88 | Menno | 723 | -0.6% |
| 89 | Woonsocket | 719 | -0.6% |
| 90 | Tripp | 712 | 0.7% |
| 91 | Kadoka | 707 | -0.4% |
| 92 | St. Francis | 705 | -1.4% |
| 93 | Canistota | 703 | 1.5% |
| 94 | Estelline | 678 | 0.3% |
| 95 | Elkton | 677 | 1.2% |
| 96 | Burke | 672 | -1.2% |
| 97 | Castlewood | 667 | 1.6% |
| 98 | Colton | 663 | 0.1% |
| 99 | Waubay | 659 | 0.2% |
| 100 | Newell | 648 | -0.4% |
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