The warnings are in place for River Stour and Smestow Brook in the Black Country and South Staffordshire, and the Upper Tame across the West Midlands.
Currently, experts are unsure on the precise areas at risk, resulting in 19 flood alerts being issued in total.
A statement issued on GOV.UK reads: "This flood alert has been issued as heavy rain and thunderstorms have been forecast for this area this afternoon, 16/08/2022 and overnight into Wednesday.
"There is uncertainty, however, over the amount of rainfall expected and the exact location of these thunderstorms.
"The largest risk is for surface water flooding affecting these areas. Additionally, given the recent hot, dry conditions any open green spaces will act like concrete and enable surface runoff."
People have also been urged to remain vigilant and avoid walking and driving through flood water.
The statement continues: "We are continuing to actively monitor the situation closely and will issue updates, and further flood alerts and warnings if necessary.
"You can monitor your local weather conditions and river levels on the GOV.UK website."
The flood risk comes in the midst of a Met Office yellow thunderstorm warning, which is slated to run until Wednesday.
A spokesman for the Met Office said: "Whilst some places will miss them, thunderstorms and areas of heavy rain seem likely to develop quite widely on Tuesday across parts of England and Wales.
"20-30 mm of rain is possible within an hour, but where areas of thundery rain become slow-moving, some places could see 50 mm in less than three hours.
"There is a low probability that higher totals could occur in a few spots over the course of the day, while hail and frequent lightning are likely additional hazards for some places.
"There is considerable uncertainty at this stage in regional and county level focus."