To better understand the Fe isotope characteristics of natural samples in the Karst area, the Fe isotope compositions of riverine suspended particulates, lake suspended particulates, lake sediments, porewaters, phytoplanktons, and aerosols in the watersheds of Lake Aha (a mineralized water system) and Lake Hongfeng (a mesotrophic water system), which are located in the Karst area, southwest China, were investigated. The studied samples displayed a variable range between δ56Fe=?2.03‰ and 0.36‰. Aerosols and phytoplanktons have similar or slightly heavier Fe isotope compositions relative to the average of igneous rocks. Fe isotope compositions of riverine Suspended Particulate Matter (SPM) were mainly affected by the types of tributaries. Suspended particulates collected from tributaries seriously contaminated with coal mine drainages displayed negative δ56Fe values (?0.89‰ to ?0.31‰) during summer, and there were significant increases of δ56Fe values in winter, except AR2, which was polluted with both coal mine drainage and sewage effluent. Characteristics of lakes have important influences on Fe isotope compositions of suspended particulates, lake sediments, and porewaters. The epilimnetic particulate Fe of Lake Hongfeng had δ56Fe=?0.04‰ to 0.13‰, while lighter Fe isotope compositions were measured for particulate Fe from Lake Aha, ranging from ?0.42‰ to ?0.09‰. Sediments collected from Hou Wu (HW) station of Lake Hongfeng have an average δ56Fe value of 0.09‰ and their corresponding porewaters have lighter Fe isotope compositions, ranging from ?0.57‰ to ?0.31‰; no significant variations have been observed. For the Liang Jiang Kou (LJK) station of Lake Aha, the content of reactive Fe and the concentration of sulfate were all high. Due to the reactive Fe recycling, including dissimilatory Fe reduction, adsorption, and Fe–sulfide formation, porewaters sampled near the sediment surface have been found to have a δ56Fe value as low as ?2.03‰ and an increase up to 0.12‰, with a burial depth of 10?cm. In contrast, an opposite variation trend was found for LJK sediments. Sediments sampled at 1-cm depth had a value of δ56Fe=?0.59‰ and decrease as low as ?1.75‰ with burial depth. This investigation demonstrated that significant Fe isotope fractionations occur in surface environments. Fe isotope compositions of particulate Fe were seriously affected by Fe sources, and Fe biogeochemical recycling has an important influence on Fe isotope fractionations in lake sediments, especially when there are significant amounts of reactive Fe and sulfate.