Bagan retains pagodas from various historic periods in Myanmar. Due to long-term exposure to open-air condition, large areas of black contaminants have formed on the mortar surfaces of these pagodas. To investigate the impact of black contaminants on the mortar, we identified the types of black contaminants and measured the parameters including temperature, moisture content, water absorption, surface hardness and ultrasonic intensity for mortar with black contaminants and for normal mortar. Comparison of these parameters shows that the black contaminants are biological crusts. Mortar affected by black contaminants exhibits the higher temperature, higher moisture content, greater water absorption, lower surface hardness, and increased efflorescence compared to normal mortar. These results indicate that that black contaminants have not only affected the appearance of the pagodas but also reduced the mechanical strength and weakened the resistance to weathering of the mortar. This study could provide a basis for the removal of black contaminants.