Freshwater ecosystems disproportionately contribute to global species biodiversity. These systems, which include lakes, rivers, and creeks, are sensitive to environmental and climatic changes, leading to dramatic shifts in local species assemblages. Global freshwater biodiversity is declining due to land use changes and pollution, which affect habitat integrity, water chemistry, and species composition. Understanding how human-driven changes in surface water chemistry affect freshwater macroinvertebrate biodiversity and algal communities is critical for guiding management and restoration efforts. Sulfate and nitrate in freshwater ecosystems can significantly affect ecological processes, biogeochemical cycling, and overall water quality. Elevated sulfate concentrations may be toxic to freshwater flora and fauna, while excess nitrate inputs can stimulate rapid phytoplankton growth. The concentrations of these chemical compounds are often influenced by land use in the surrounding watershed and are subsequently transported to streams as runoff. Our project focuses on McDiffett Creek in Kansas, which is surrounded primarily by agricultural land, and the Blue River in Oklahoma, which is largely used for recreation and protected under two conservation programs. McDiffett Creek has experienced greater ecological disturbance than Blue River. Using data from the National Science Foundation’s (NSF) National Ecological Observatory Network (NEON), we analyzed sulfate and nitrate concentrations as indicators of agricultural runoff. Nitrate and sulfate data were collected bi-monthly from 2017 to 2023. Taxonomic and biomass data for local phytoplankton communities and macroinvertebrate taxonomic data were analyzed for the same time period. Our data indicate no significant difference in nitrate concentrations between sites, while sulfate concentrations were four times higher in the agricultural basin. This suggests that agricultural landscapes may increase sulfate levels within nearby waterways. Despite having lower macroinvertebrate species richness, Shannon diversity was higher at the agricultural stream. Conversely, the agricultural site had twelve times higher algal biomass than the non-agricultural stream, but lower species diversity. These findings highlight how land use can influence organismal communities in complex ways, affecting both species richness and biomass.