Expect clouds, rain and wind today in Winnipeg. (Brett Purdy/CBC)

An ugly day is in store across much of southern Manitoba with a rainfall warning in place for the southwest.

Anywhere between 20-50 millimetres is expected to fall in that area, while the Winnipeg region should see 15 to 20 mm with a high of just 16 C.

It will be blustery as well, with cool northeast winds hitting about 30 km/h in the city.

On the lakes, however, it will be much worse.

Environment Canada has issued a strong wind warning for Lake Winnipeg and Lake Manitoba.

The winds will blow east  at about 27 km/h and increase to northeast about 37 km/h later in the morning and to 55 km/h in the late afternoon. But there will likely be gusts that push the wind speed to nearly 75 km/h at times.

It will back off to about 45 km/h from the northwest late this evening and diminish to 27 km/h by Friday morning, but strengthen again to 46 km/h Friday evening.

A low pressure system in southeastern Saskatchewan is to blame for the bad weather, Environment Canada says. The system will track eastward into southwestern Manitoba this morning before moving off into northwestern Ontario.

The system is currently bringing rain with embedded thunderstorm activity, giving way to heavy downpours, Environment Canada states in a weather alert.

"Localized flooding in low-lying areas is possible," the alert says.

The rain is expected to taper off across the warning area later this afternoon or early this evening.