Changes in the levels of biogenic silica (BSi%) in lake sediments have been widely used in order to study lake productivity and palaeoclimatic changes. However, the provenance of biogenic silica (BSi) needs to be investigated for each lake, especially for large lakes, as does the relationship between levels of BSi and relevant environmental factors. In this study, we measured the percentage of BSi contained in lake sediments, river sediments, and surface soils within the Lake Qinghai catchment, and compared the quantities and shapes of diatoms and phytoliths before and after the extraction processes. The results suggest that BSi in lake sediments is primarily derived from endogenous diatoms; therefore, BSi levels can be used to reflect the changes in primary productivity within the lake. Further comparisons showed that on long-term timescales, the variations in BSi% are generally consistent with those in total organic carbon (TOC) and grain size, reflecting the dominant impacts of precipitation on primary productivity in Lake Qinghai. On short-term timescales, however, the relationship between BSi% and TOC and that between BSi% and grain size are not clear or stable. For example, BSi% sometimes covaried with grain size, but it was sometimes out of phase with or even inversely related to grain size. We speculate that both climate and environmental processes, such as the dilution effect, influence short-term BSi% and its related environmental significance. As a result, BSi% should be used selectively as an indicator of climatic changes on different time scales.