This material contains the livestock farm dataset used in the study, covering the 2011–2023 period at the municipality level, together with the calculation procedures adopted to estimate manure production, nitrogen loads, methane production, and electricity generation potential. The repository also includes the input parameters, equations, assumptions, literature references, and a README file describing the structure and organization of the provided materials. In addition, a geodatabase archive is provided containing the main spatial datasets and geostatistical outputs used in the GIS workflow, including municipalities, regions, Nitrate Vulnerable Zones (NVZs), emerging hotspot analysis results, trend analysis outputs, and forecasting layers.