Under the rules, it is mandatory for all farmers to maintain good practice to prevent water pollution incidents.
Farming-related pollution incidents can harm wildlife in rivers and seas, impact the economy and result in higher bills from increased water treatment.
The rules aim to promote good practice in managing fertilisers and manures and encourage land managers to take reasonable precautions to prevent diffuse pollution from runoff or soil erosion.
They are also required to plan each application of manure or fertilisers, based on soil tests, to meet but not exceed crop and soil needs.
Environment Minister Therese Coffey said: “This is a really important opportunity for farmers to reduce pollution in watercourses. In following these rules, farmers will be able to help reduce pollution incidents, improve water quality and save money through some efficient use of resources.”