Agriculture alters the biogeochemical cycling of nutrients such as nitrogen (N), phosphorus (P), and silicon (Si) which contributes to the stoichiometric imbalance among these nutrients in aquatic systems. Limitation of Si relative to N and P can facilitate the growth of non-siliceous, potentially harmful, algal taxa which has severe environmental and economic impacts. Planting winter cover crops can retain N and P on the landscape, yet their effect on Si concentrations and stoichiometry is unknown. We analyzed three years of biweekly concentrations and loads of dissolved N, P, and Si from subsurface tile drains and stream water in two agricultural watersheds in northern Indiana. Intra-annual patterns in Si concentrations and stoichiometry showed that cover crop vegetation growth did not reduce in-stream Si concentrations as expected, although, compared to fallow conditions, winter cover crops increased Si:N ratios to conditions more favorable for diatom growth. To assess the risk of non-siliceous algal growth, we calculated a stoichiometric index to quantify biomass growth facilitated by excess N and P relative to Si. Index values showed a divergence between predicted algal growth and what we observed in the streams, indicating other factors influence algal community composition. The stoichiometric imbalance was more pronounced at high flows, suggesting increased risk of harmful blooms as climate change increases the frequency and intensity of precipitation in the midwestern U.S. Our data include some of the first published measurements of Si within small agricultural watersheds and provide the groundwork for understanding the role of agriculture on Si export and stoichiometry.