| WQS0001 | Iowa River | Iowa City | 3147 |
| WQS0002 | Clear Creek | Coralville | 98 |
| WQS0003 | Clear Creek | Oxford | 61 |
| WQS0004 | Clear Creek | Homestead | 8 |
| WQS0005 | English River | Kalona | 576 |
| WQS0006 | Iowa River | Lone Tree | 4293 |
| WQS0007 | Cedar River | Conesville | 7787 |
| WQS0008 | Slough Creek | Orchard | 6 |
| WQS0009 | Otter Creek | Elgin | 46 |
| WQS0010 | Skunk River | Augusta | 4312 |
| WQS0011 | Clear Creek | Homestead | 10 |
| WQS0012 | Slough Creek | Orchard | 5 |
| WQS0013 | Beaver Creek | Bassett | 17 |
| WQS0014 | Beaver Creek | Colwell | 7 |
| WQS0015 | Otter Creek | Elgin | 26 |
| WQS0016 | Otter Creek | West Union | 15 |
| WQS0017 | Brockamp Creek | Fort Atkinson | 8 |
| WQS0018 | Roberts Creek | Elkader | 116 |
| WQS0019 | South Chequest Creek | Douds | 31 |
| WQS0020 | Mississippi River Pool 16 | Fairport | 99300 |
| WQS0021 | Rapid Creek | Iowa City | 6 |
| WQS0022 | Rapid Creek | Iowa City | 3 |
| WQS0023 | Wapsipinicon River | De Witt | 2336 |
| WQS0024 | South Fork Iowa River | New Providence | 224 |
| WQS0025 | Catfish Creek | Dubuque | 41 |
| WQS0026 | Catfish Creek | Dubuque | 13 |
| WQS0027 | Lime Creek | Brandon | 41 |
| WQS0028 | Des Moines River | Boone | 56 |
| WQS0029 | Water supply well | Boone | 56 |
| WQS0030 | Groundwater / Spring | Delaware | 15 |
| WQS0031 | Groundwater / Spring | Elkader | 103 |
| WQS0032 | Middle Raccoon River | Panora | 440 |
| WQS0033 | Des Moines River | Keosauqua | 14038 |
| WQS0034 | Cedar Creek | Batavia | 248 |
| WQS0035 | Miller Creek | La Porte City | 23 |
| WQS0036 | Thompson River | Davis City | 701 |
| WQS0037 | East Nishnabotna River | Brayton | 278 |
| WQS0038 | Ioway Creek | Ames | 196 |
| WQS0039 | Boone River | Goldfield | 420 |
| WQS0040 | Boyer River | Logan | 850 |
| WQS0041 | Little Sioux River | Turin | 760 |
| WQS0042 | Maple River | Mapleton | 669 |
| WQS0043 | Floyd River | James | 886 |
| WQS0044 | East Nishnabotna River | Riverton | 1105 |
| WQS0045 | Des Moines River | Stratford | 5452 |
| WQS0046 | Walnut Creek | Prairie City | 20 |
| WQS0047 | Walnut Creek | Prairie City | 7 |
| WQS0048 | Tipton Creek | Hubbard | 72 |
| WQS0049 | Chequest Creek | Douds | 104 |
| WQS0050 | West Fork Crooked Creek | Washington | 93 |
| WQS0051 | Beaver Creek | Eldora | 70 |
| WQS0052 | McLoud Run | Cedar Rapids | 2 |
| WQS0053 | Walnut Creek | Kelley | 11 |
| WQS0054 | Drainage tile, Walnut Creek | Ames | 2 |
| WQS0055 | Drainage tile, Tipton Creek | Sherman | 7 |
| WQS0056 | Drainage tile, Tipton Creek | Sherman | 47 |
| WQS0057 | | | 1 |
| WQS0058 | Willow Creek | Kellogg | 1 |
| WQS0059 | Perry Pond | Kellogg | 1 |
| WQS0060 | Frye Oxbow | Webster City | 76 |
| WQS0061 | Soldier River | Pisgah | 405 |
| WQS0062 | Mill Creek | Cherokee | 295 |
| WQS0063 | Yellow River | Ion | 221 |
| WQS0064 | Upper Iowa River | Dorchester | 778 |
| WQS0065 | Little Sioux River | Little Sioux | 4506 |
| WQS0067 | Rock River | Rock Valley | 1614 |
| WQS0068 | Soap Creek | Floris | 188 |
| WQS0069 | Wapsipinicon River | Central City | 1282 |
| WQS0070 | Wolf Creek | Dysart | 299 |
| WQS0071 | Mud Creek | Vinton | 44 |
| WQS0072 | North English River | North English | 294 |
| WQS0073 | Powell Creek | Storm Lake | 68 |
| WQS0074 | Cedar Creek | Pocahontas | 55 |
| WQS0075 | West Nishnabotna River | Harlan | 313 |
| WQS0076 | Drainage Ditch | Coralville | 1 |
| WQS0079 | Nishnabotna River | Hamburg | 1 |
| WQS0080 | Saturated Buffer | Adair | 85 |
| WQS0081 | Boone River | Webster City | 844 |
| WQS0082 | North Raccoon River | Jefferson | 1619 |
| WQS0083 | Shell Rock River | Shell Rock | 1746 |
| WQS0084 | Cedar River | Janesville | 55872 |
| WQS0086 | South Raccoon River | Redfield | 1 |
| WQS0087 | Iowa River | Wapello | 1 |
| WQS0088 | West Fork Cedar River | Finchford | 846 |
| WQS0089 | Nodaway River | Clarinda | 1 |
| WQS0090 | Village Creek | Lansing | 60 |
| WQS0091 | Waterloo Creek | Dorchester | 48 |
| WQS0092 | Des Moines River | Des Moines | 1 |
| WQS0093 | Beaver Creek | Johnston | 1 |
| WQS0094 | Mud Creek | Bondurant | 1 |
| WQS0095 | Camp Creek | Mitchellville | 1 |
| WQS0096 | Fourmile Creek | Ankeny | 1 |
| WQS0097 | Fourmile Creek | Des Moines | 1 |
| WQS0098 | Raccoon River | Des Moines | 1 |
| WQS0099 | South Skunk River | Bondurant | 1 |
| WQS0100 | Walnut Creek | Des Moines | 1 |
| WQS0101 | Mud Creek | Benton County | 2 |
| WQS0102 | Mud Creek | Benton County | 12 |
| WQS0103 | Mud Creek | Benton County | 1 |
| WQS0104 | Carnarvon Creek | Lake View | 11 |
| WQS0105 | Benton County DOT Ditch 1 | | 1 |
| WQS0106 | Benton County DOT Ditch 2 | | 1 |
| WQS0107 | Eagle Creek Oxbow | Woolstock | 1 |
| WQS0108 | Prairie Creek/Boone River Oxbow | Lu Verne | 1 |
| WQS0109 | Johnson County Poor Farm | Iowa City | 1 |
| WQS0110 | Maquoketa River | Green Island | 1859 |
| WQS0111 | Bloody Run Creek | Marquette | 34 |
| WQS0112 | Mud Creek Wetland Outlet | Keystone | 2 |
| WQS0113 | Decorah Fish Hatchery | Decorah | 1 |
| WQS0114 | Bloody Run Creek Headwaters | Monona | 1 |
| WQS0115 | Des Moines River | Ottumwa | 1 |
| WQS0116 | Iowa Great Lakes 1 | Spirit Lake | 1 |
| WQS0117 | Iowa Great Lakes 2 | Milford | 1 |
| WQS0118 | Maquoketa River | Maquoketa | 1553 |
| WQS0119 | Wapsipinicon River | Anamosa | 1575 |
| WQS0120 | East Nishnabotna | Atlantic | 436 |
| WQS0121 | East Nishnabotna River | Red Oak | 894 |
| WQS0122 | Upper Iowa River | Lime Springs | 181 |
| WQS0123 | Upper Iowa River | Bluffton | 367 |
| WQS0124 | Floyd River | Alton | 268 |
| WQS0126 | Wapsipinicon River | Tripoli | 346 |
| WQS9901 | Morgan Creek Oxbow | Cedar Rapids | 14 |
| WQS9903 | | | 0 |
| WQS9904 | | | 1 |
| WQS9931 | Groundwater / Spring | Elkader | 103 |
| WQS9953 | | | 1 |
| WQS9994 | | | 1 |
| WQS9995 | | | 1 |
| WQS9996 | | | 1 |
| WQS9997 | | | 1 |
| WQS9998 | | | 1 |