Your kidneys filter waste products from your blood while retaining what your body needs — including proteins. However, some diseases and conditions allow proteins to pass through the filters of your kidneys, causing protein in urine. Conditions that can cause a temporary rise in the levels of protein in urine, but don't necessarily indicate kidney damage, include: 1  Dehydration. 2  Emotional stress. 3  Exposure to extreme cold. 4  Fever. 5  Strenuous exercise.