:Benthic algae comprise a diversity of taxonomic lineages and produce important biochemical compounds required by higher trophic levels. Chief among these compounds are essential fatty acids (EFAs) that aquatic consumers require for their metabolic and reproductive processes. However, habitat changes from anthropogenic activities, namely, agriculture, can affect not only which species of algae may be present but also the quantity and quality of EFAs they produce. This study aims to evaluate how benthic algal taxonomic composition and EFA concentrations vary in streams affected by agriculture and remediation through stream-associated best management practices (BMPs). The study was undertaken in the Upper Delaware River watershed in New York state, in which BMPs have been installed over multiple years (= BMP age). Some results indicate that BMPs were able to reduce effects of agriculture. Changes in benthic algal assemblages, the proportions of algal taxonomic groups, and in specific taxonomic members were not significant. The proportion of diatoms in assemblages decreased with increasing agricultural effects (F = 6.313, P = 0.001). Conversely, the proportion of chlorophytes increased in agriculturally affected streams (F = 9.336, P < 0.001). Changes in taxonomic composition were associated with changes in various EFA compound concentrations. Agricultural streams had higher concentrations of total EFAs along with more chlorophytes (r = −0.268, P = 0.010) and fewer diatoms (r = 0.270, P = 0.009) than did reference or minimally affected streams. Particularly, agricultural streams had greater concentrations of key EFAs such as eicosapentaenoic acid and docosahexaenoic acid. However, there were no differences among assemblage's nutritional quality (Σω3/Σω6). The data presented here suggest that analyzing shifts in algal taxonomic groups in conjunction with measurements of fatty acids in broad EFA groups may provide more information when characterizing algal assemblages than examination of algal taxa or analysis of EFA compounds alone.