The objectives of this study were to compare estimates of greenhouse gas emissions (GHG) as CH4 (enteric-manure), N2O (manure), and CO2 (fuel and energy use), the use of water and soil, the excretion of nutrients in manure, and feed efficiency from Mexican intensive dairy farms. Data from 26 dairy farms were analysed with a multivariable cluster analysis. Three grades of intensifications were identified (low, medium and high). Mathematical models were used to estimate GHG. Feed efficiency (kg milk per kg DMI) was better in high intensive production systems. Enteric methane was identified as the major source of GHG in all types of systems. High intensive dairies generated the lowest emissions of CH4, N2O and CO2 equivalent by unit of product, 18.6 g, 0.12 g and 828 g, respectively. Water footprint was lower in low intensive dairies using 427 L of water/L of milk. Cropland was highest in intensive systems but milk yield per area was better (30,938 kg/ha). Excretions of N, P, and K were lower in intensive dairies per kg of milk, at 13.2, 2.4, and 6.4 g, respectively. As intensification in the dairy system increased feed efficiency (kg milk/kg DMI) was better. Per unit of product (kg of milk), dairies with the highest intensification generated the lowest GHG emissions, nutrient excretion values and land and water use as compared to dairies with medium and low intensification. Increasing intensification and therefore feed efficiency of Mexican dairy systems could help to decrease GHG emissions, natural resources use and nutrient excretion.