Agricultural land use is essential for food production, but intensively managed landscapes can considerably alter the “critical zone,” which is the thin, life-supporting layer of Earth’s surface from the tops of the trees to the bottom of the groundwater. Excess inputs of nutrients from chemical fertilizers and manures used in agriculture that enter aquatic environments can trigger algal blooms, which can have severe impacts on humans and ecosystems. Successful management of nutrient pollution requires understanding river systems, which transport excess nutrients to the ocean but can also sequester or transform them in the water column, channel bed sediments, floodplains, or reservoirs. We investigated the role of reservoirs in controlling water quality in agricultural critical zones and found that reservoir bed sediments can act as both nutrient sinks or sources for rivers. A long‐term nutrient mass balance for an Illinois reservoir showed that sediment processes consistently removed nitrogen pollution from the water column over time. Phosphorus contamination was initially stored in reservoir sediments, but this storage capacity was exhausted and legacy phosphorus was subsequently released from the reservoir. Thus, reservoirs in agricultural critical zones can act as a sink for nitrogen but can change from a sink to a source for phosphorus over decadal timescales. Our study showed that agricultural reservoirs could become important sources for nutrient pollution in the future.