Freshwater harmful algal blooms (HABs), driven by nutrient inputs from anthropogenic sources, pose unique risks to human and ecological health worldwide. A major nutrient contributor is agricultural land use, specifically tile drainage discharge. Small lakes and ponds are at elevated risk for HAB appearance, as they are uniquely sensitive to nutrient input. HABs introduce exposure risk to microcystin (MC), hepatotoxic and potentially carcinogenic cyanotoxins. To investigate the impact of anthropogenic land use on small lakes and ponds, 24 sites in central Ohio were sampled over a 3-month period in late summer of 2015. MC concentration, microbial community structure, and water chemistry were analyzed. Land use intensity, including tile drainage systems, was the driver of clustering in principle component analysis, ultimately contributing to nutrient deposition, a driver of HABs. Relative abundance of HAB-forming genera was correlated with elevated concentrations of nitrate and soluble reactive phosphate. One location (FC) showed MC concentrations exceeding 875 μg/L and large community shifts in ciliates (Oligohymenophorea) associated with hypoxic conditions. The prokaryotic community at FC was dominated by Planktothrix sp. These results demonstrate the impact of HABs in small lakes and ponds, and that prevailing issues extend beyond cyanotoxins, such as cascading impacts on other trophic levels.