- Bear Creek (Upper Iowa River)
- Bear Creek (Yellow River)
- Beaver Creek (Cedar River)
- Beaver Creek (Polk County, Iowa), a tributary of the Des Moines River
- Big Sioux River
- Blue Earth River
- Boone River
- Boyer River
- Broken Kettle Creek
- Canoe Creek
- Catfish Creek
- Cedar River
- Chariton River
- Cloie Branch
- Competine Creek
- Davis Creek
- Deep River
- Des Moines River
- Elk River
- English River
- Flint River
- Floyd River
- Fox River
- French Creek
- Grand River
- Iowa River
- Lime Creek
- Little Cedar River
- Little Fox River
- Little Maquoketa River
- Little Ocheyedan River
- Little River
- Little Rock River
- Little Sioux River
- Little Turkey River (Clayton County, Iowa)
- Little Turkey River (Fayette County, Iowa)
- Little Wapsipinicon River (north)
- Little Wapsipinicon River (south)
- Maple River
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- Maquoketa River
- Middle River
- Mississippi River
- Missouri River
- Mosquito Creek
- Nishnabotna River
- Nodaway River
- Norfolk Creek
- North Fabius River
- North River
- Ocheyedan River
- Pea's Creek
- Perry Creek
- Pine Creek (Canoe Creek)
- Pine Creek (Upper Missouri River)
- Platte River
- Raccoon River
- Rock River
- Rutt Branch
- Shell Rock River
- Skunk River
- Soldier River
- South River
- Squaw Creek
- Tarkio River
- Thompson River
- Thunder Creek
- Trout River
- Turkey River
- Upper Iowa River
- Volga River
- Wapsipinicon River
- Waterloo Creek
- Weldon River
- West Fork of the Little Sioux River
- White Breast Creek
- White Fox Creek
- Winnebago River
- Wyaconda River
- Yellow River
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