Eutrophication of natural water is a universal problem. Nitrogen (N) and phosphorus (P) from agricultural runoff are the main sources of nutrient input, provided that emissions from industrial point sources (IPS) are under control. Therefore, it is of great environmental importance to reduce pollution associated with agricultural runoff as a means of regulating eutrophication levels in natural water. Numerous methods proposed for treating agricultural runoff can be classified into three categories: source control, process control, and end treatment. In this review, major technologies for N and P control from agricultural runoff are summarized along with discussion of newly proposed technologies such as biochar biomimetics and microbial catalyst. Because agricultural runoff (from farmlands to receiving waters) is a complicated pollution process, it is difficult to regulate the nutrients discharged via such process. This review will thus offer a comprehensive understanding on the overall process of agricultural runoff and eutrophication to help establish control strategies against highly complicated agricultural non-point sources.