(1) Background: the broadcast is an outdated fertilization method with a low fertilizer-utilization rate and environmental problems, which seriously restricts the development of agriculture. (2) Methods: Under a machine-transplanted rice with side-deep fertilization (MRSF) mode, five treatments were applied: 0 cm (D0), 5 cm (D5), 7.5 cm (D7.5), and 10 cm (D10), comprising four different depths of fertilization, and no fertilization (CK). The yield, the accumulation of N and P in the straw and in grains of rice, concentrations of N and P in the surface water, ammonia (NH3) volatilization, and s...