To gain a better understanding of the impact from the land-use change in the Huixian karst wetland system, we analyzed soil microflora, enzyme activities, and physicochemical properties from three land-use types (natural wetland, paddy field, and dry farmland). The results showed that soil pH, soil organic carbon, total nitrogen, cation exchange capacity, exchangeable Ca and Mg, and the cellulase and alkaline phosphatase activities in the dry farmland were significantly lower than those in the paddy field and natural wetland (p<0.05). However, soil pH, soil organic carbon, total nitrogen, cation exchange capacity, exchangeable Ca and Mg, and the cellulase and alkaline phosphatase activities made no significant difference to the paddy field and the natural wetland (p>0.05). Moreover, the soil microbial biomass carbon and nitrogen in the dry farmland were also lower than those in the paddy field and natural wetland, although no significant differences were observed (p>0.05). This suggests that, in the alkali condition, natural wetland with high biomass and weak microbial activity may be an important carbon sink. In the CCA biplot, it can be seen that the natural wetland cluster intersects with the paddy field cluster and the dry farmland cluster in the same quadrant (although the paddy field and the dry farmland clusters are separate). Therefore, we concluded that the natural wetland usually was reclaimed as paddy field or dry farmland directly for agricultural output in the Huixian karst wetland system. The paddy field has a waterlogged condition and shows the similar results to natural wetland, which can be regarded as artificial wetland. In view of the similar ecosystem services by paddy fields as substitutes of natural wetland, if the degradation trend of natural karst wetland can’t be reversed, the paddy field should be preserved in the Huixian karst wetland system for its ecosystem service.