The Federal Hydrometereological Institute issued a red warning for flooding on Friday.
The first wave of floods started on Thursday and caused many rivers to flood or have their levels significantly increased.
Hundreds of objects were at least partially flooded. Otes was hit the hardest, where fire cars are used to evacuate tens of people and sandbags placed to prevent houses from flooding.
The flash flooding caused electrical substations to malfunction, leaving a large part of Sarajevo's outskirts without power.
The rain is forecast to not completely stop until Monday.