Technical Abstract: Injection of liquid swine manure disturbs surface soil, so that runoff from treated lands can transport sediment and nutrients to surface waters. With a field study we determined the effect of two swine manure application methods on phosphorus (P) fate in a corn (Zea mays L.)-soybean (Glycine max L. Merr.) production system, with and without a winter rye (Secale cereale L.) – oat (Avena sativa L.) cover crop. Treatments included: i) no manure; ii) knife injection; and iii) low-disturbance injection, each with and without the cover crop. Simulated rainfall runoff was analyzed for dissolved reactive P (DRP) and total P (TP). Rainfall was applied 8 d after manure application (early November) and again in May after emergence of the corn crop. Manure application increased soil bioavailable P in the 20-30 cm layer following knife injection, while the highest P levels were detected in the 5-20 cm layer following low-disturbance injection. The low-disturbance system caused less damage to the cover crop, so that P uptake was more than three-fold greater. Losses of DRP were greater in both the fall and spring following low-disturbance injection; however, application method had no effect on TP loads in runoff in either season. The cover crop reduced fall TP losses from plots with manure applied by either method. In the spring, DRP losses were significantly higher from plots with the recently killed cover crop, but TP losses were not affected. Low-disturbance injection of swine manure into a standing cover crop can minimize both damage to the cover and losses of P to surface runoff, while providing optimum P availability to a subsequent agronomic crop.