Phosphorus (P), an essential nutrient in crop and livestock agriculture, can cause and accelerate freshwater eutrophication. Intensification of farming systems has resulted in local accumulations of P in some agricultural watersheds with related increases in P runoff. In most cases, continual land application of manure at rates exceeding crop P removal is the proximate cause of P runoff. To mitigate associated water quality impairments, P‐based agricultural best management practices (BMPs) are now becoming a part of farm nutrient planning. This planning involves the selection, timing, and implementation of source and transport BMPs at field, farm, and watershed scales. Source measures include balancing P imports and exports, improved livestock feed management, chemical and physical treatment of manures, appropriate rate, method, and timing of land application based upon regular soil and manure testing, adequate manure storage and transport infrastructure, and composting. Transport measures aim to reduce runoff and erosion via practices such as conservation tillage, contour ploughing, and vegetative filter strips. To be effective, these measures must be carefully selected and targeted to areas at greatest risk to P loss. This vulnerability can be identified and ranked by P indices, which account for source and transport factors controlling P loss. We demonstrate that the P Index can provide flexible yet reliable manure management and provide farmers with options to minimise the risk of P loss from several farms in Pennsylvania, United States. Overall, a comprehensive and holistic approach to manure management can decrease P transfers from land to water.