The karst region in southwestern China is a typical region with fragile ecological environments, and the coordination of regional agricultural development and environmental protection faces enormous challenges. Based on the soil and hydrological characteristics of karst in southwestern China, this study summarized water-related environmental issues caused by agricultural activities in this karst region. Agriculture in the karst hills is more likely to cause soil and nutrient losses due to the fast hydrological flow through special karst structures with high permeability. Thus, this review emphasized the impacts of agricultural development on the riverine biogeochemical cycles of elements based on previous studies. Meanwhile, the carbon cycle is also strongly impacted by agricultural activities in this karst region due to enhanced carbonate weathering by nitric acid from the nitrification of ammonium. This weathering mechanism represents a net source of atmospheric CO2 and might impact regional and global carbon cycling in the Anthropocene. Based on the results summarized in this study, we advocate that in the future, better management of agricultural land, improvement of fertilizer use efficiency, and boosting of nutrient recycling rate should be taken into account for reducing nutrient losses and water quality deterioration. Targeted management of local agricultural practices along with guidance from scientific research results is needed to be devoted to sustainable development of agriculture and economies while protecting water environment.