Dissolved silicon (DSi) in natural waters plays important roles in sustaining continent, riverine and ocean ecosystems. It is a necessary nutrient for the growth and reproduction of aquatic plants and phytoplankton, especially diatoms. The composition of dissolved silicon in river systems is complex and depends on physical, chemical, and biological processes that occur in drainage basins and rivers. In this study, a typical karst watershed located in Guizhou Province, Southwest China was selected as the study area to reveal the characteristics of DSi transport and discuss seriously environmental effects on the variation of DSi concentration. The objects of this research were to monitor the dynamic characteristics of dissolved silicon in wet deposition, rainfall-runoff processes and baseflow process in the dry and wet seasons during the whole year and to discuss about serious environmental effects on the variation of DSi concentration. Results showed that (1) The greater the rainfall, the smaller the DSi concentration during the wet deposition. DSi concentration in the wet season was higher than that in the dry season. DSi concentration and discharge in surface water were more easily responded by rainfall-runoff process than in groundwater. (2) The deposition flux and export flux of DSi showed evident differences in the wet and dry seasons. DSi deposition flux in the wet season accounted for 69.5%, and export load of surface water and groundwater accounted for 98.1% and 51.4% of the whole year, respectively. (3) The study area had a slow weathering rate of silicate minerals which was mainly controlled by carbonates and evaporite rates. DSi concentration was significantly affected by man-made reservoir as the results showed that the DSi concentration dropped by 29% and 70% in the dry and wet seasons, respectively. The study is conducive to a more comprehensive understanding of the silicon biogeochemical cycle in terrestrial ecosystems. In future studies, long-term studies on the effects of agricultural activities and land use patterns on the supply of nutrients in the watershed are needed to predict the change of phytoplankton community with the dynamic change of DSi concentration from a long-term perspective. In addition to DSi monitoring, BSi monitoring should be added to further study the silicon cycling process and related environmental effects in terrestrial ecosystems.