Harmful algal blooms are becoming a major global environmental problem. These blooms, resulting primarily from nutrient over-enrichment in aquatic systems, cause depletion of oxygen, degradation of ecosystems, fish kills, and release of toxins harmful to humans and animals. The prime nutrients responsible for these events include nitrogen (N) and phosphorus (P), which are present in sufficient quantities in most fertilizer formulations used in agriculture. Such resource imbalances expressed in terms of nutrient runoff occur as global food production increases and such have since cumulated into perhaps the single most important element of eutrophication. This chapter addresses the intricacy of the connection between agricultural practices and harmful algal bloom formation. It covers the sources and pathways of nutrient inputs, the ecological mechanisms connecting such nutrients to bloom formation, empirical observations from various ecosystems, and potential mitigation pathways. The goal is to provide a converging view of what the “Agricultural Nexus” between farming, nutrient loading, and degradation of water quality. This study, The Agricultural NEXUS: How Farming Practices Increase Nutrient Inputs and Harmful Algal Bloom Indices, also examines the important connection between agricultural land use and increased nutrient loading, particularly nitrogen and phosphorus, in aquatic systems. By combining data from watershed monitoring, remote sensing, and farm management records, we pinpoint key farming practices. These include synthetic fertilizer application, manure management, and tillage methods that lead to greater nutrient runoff. We present a HAB index framework that links these practices to bloom frequency, duration, and toxicity. Our findings show that heavily managed agricultural areas have much higher HAB indices, resulting from both diffuse and point-source nutrient inputs. The paper highlights the urgent need for integrated land–water management strategies, such as best management practices (BMPs), policy changes, and precision agriculture, to reduce the negative impacts of farming on water quality and ecosystem health.