Streams play vital roles in surrounding communities and provide essential ecosystem services. The protection of streams is important, they are legally protected under the Clean Water Act, and they can be monitored through the continuous analyses of biological data, such as algal or other aquatic communities. The goals of this study were to analyze the long-term recovery of Tobler Creek, a recovering agricultural stream on the site of a National Historic Landmark, and yield comparisons to a local low-impact stream, Murder Creek, located within the Oconee National Forest. In 2011, Tobler Creek exceeded reference criteria values for total phosphorus (TP) but met the nitrate nitrogen criteria. With an 11-year recovery period, Tobler Creek met both nutrient reference criteria. In 2022, periphyton samples were collected according to standard protocols, confirming that diatoms are the dominant algal group in the community. With recovery, Tobler Creek showed an increase in diatom species richness (χ2 = 116.11, df = 5, p < 0.01) but this was significantly lower than the values documented in Murder Creek. The multi-metric index (MMI), calculated using diatom community analysis to estimate ecological health, indicated that Tobler Creek experienced degradation from 2011 to 2022 (χ2 = 55.97, df = 5, p < 0.05) and is below the regional 25th percentile. The percentage of sediment-tolerant taxa (surirelloid, naviculoid, and nitzschoid) was significantly higher in Tobler Creek in 2022 (χ2 = 500.96, df = 5, p < 0.01) compared to Murder Creek in 2022 (t = −4.67, df = 10, p < 0.01). Despite a reduction in nutrients given the 42-year recovery period, the diatom community in Tobler Creek was significantly different than other regional protected streams. Ecological degradation of the habitat was likely driven by sedimentation due to run-off in the recovering agriculture stream. These findings highlight the importance of protecting water quality, as the recovery of nutrients can be a decades-long process overlayed with many potentially new stressors influencing aquatic organisms.