Karaftu Cave in the northwest of Divandareh, includes four floors plus an underground area. The bat hall and its underground area are covered with guano deposits. 14C dating indicates the onset of guano deposition is about 14260±50 BP years, and its average accumulation rate is about 4.1 mm/yr for depths of 360 to 205 cm. Bacterial and fungal metabolisms decay guano, release acids, and disperse large amounts of microorganisms inside the cave. Interactions between acids and guano caused leaching, dissolution, change in the distribution and abundance of elements, which leads to the formation of secondary minerals in guano. These variations in minerals and elements also depend on the local climatic conditions. Distribution of elements in the Ce/Ce* verse Pr/Pr* diagram and correlation coefficient between Ce and Mn display three different paleoclimate conditions (dry, wet, and dry) during the accumulation of the guano. Also, dolomite, phosphate, and iron oxide minerals have been formed during the passage of water through bedrock beneath the guano. This water is unsuitable for drinking and harmful to the organisms in the region. Effect of these acids on the substrate also leads to collapse of the cave floor, generation of a new underground, fall in the groundwater level, change in the groundwater drainage system, drying of springs around the cave, loss of green cover, and a negative impact on the ecosystem in the region. To keep the cave environment clean and remove these problems, it is better to harvest guano and use it as fertilizer.