Nutrients can load directly to either the epilimnion or metalimnion of lakes via either differential inflow depths of tributaries or intentional fertilization of discrete strata. We evaluated the differential effects of epilimnetic versus metalimnetic nutrient loading using 17-m-deep mesocosms that extended into the deep chlorophyll layer of oligotrophic Pettit Lake in the Sawtooth Mountains of Idaho. Addition of nitrogen plus phosphorus stimulated primary production nearly identically (2.4- to 4-fold on different dates) in both treatments, with the production peaks occurring in the strata where nutrients were added. The metalimnetic fertilization, however, resulted in equal or greater stimulation of chlorophyll a and phytoplankton biovolume than when nutrients were added directly to the epilimnion. Periphyton growth was stimulated 10–100 times more by epilimnetic fertilization than by metalimnetic fertilization and diverted nutrients from the planktonic autotrophs. These results suggest that the development of deep chlorophyll layers may be influenced by plunging river inflows that carry nutrients to the metalimnion and that metalimnetic lake fertilization may be useful as a tool for increasing lake productivity while reducing the impact on water quality.