Mobilization of DNA by horizontal gene transfer (HGT) is an important process in the evolution of many organisms because it allows the recipient lineage to rapidly acquire metabolic innovations and adapt to new ecological niches. However, the significance of HGT in specific ecosystems remains poorly understood. In this review, we present major findings that illustrate how HGT affects managed ecosystems, such as farmlands, orchards, pastures, and managed grasslands. First, acquisition of functions via HGT can lead to the emergence of novel or more virulent pathogens and parasites of crops by allowing them to circumvent host defenses and currently used pest management approaches. Second, HGT of antibiotic resistance genes from the application of wastewater effluent for irrigation or manure as fertilizer can facilitate the emergence of highly resistant microbial lineages. Lastly, HGT can enhance the functional diversity of microbial communities and potentially influence biogeochemical processes. Characterization of lineages possessing horizontally acquired genetic material and their ecology will aid in enhancing the productivity and sustainability of managed ecosystems. We conclude with recommendations for key research directions that will advance our understanding of the causes and consequences of HGT in managed ecosystems.