Land application of farm dairy effluent (FDE) to pasture soils is the preferred practice in New Zealand. Recently, a new FDE treatment technology has been developed to recycle the water for washing the yard Cameron and Di (J Soils Sediments 2018). Here we report a lysimeter study to compare the leaching losses of Escherichia coli, phosphorus (P), and nitrogen (N) and emissions of greenhouse gases from the treated FDE compared with the untreated original FDE. Lysimeters were collected from a Balmoral silt loam soil (Typic Dystrudept, USDA) and installed in a field trench facility. Treatments included (1) treated effluent (TE), (2) a mixture of TE and recycled water (M), (3) untreated original FDE (FDE), and (4) water as control. The effluents were applied at a surface application rate of 24 mm on each lysimeter in May and again in September 2017. Measurements included leaching losses of E. coli, total phosphorus (TP), dissolved reactive phosphorus (DRP), total mineral nitrogen (TN), ammonium-N (NH4+-N), and nitrate-N (NO3−-N); emissions of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4); herbage yield; and N uptake. The results showed that E. coli, TP, and DRP leaching losses from the TE were 1.31 × 1010 cfu/ha, 0.26 kg P/ha, and 0.009 kg DRP/ha and from M treatments were 6.96 × 108 cfu/ha, 0.18 kg P/ha, and 0.004 kg DRP/ha, respectively, which were significantly (P < 0.05) lower than those from the FDE which were 4.21 × 1010 cfu/ha, 1.75 kg P/ha, and 0.034 kg DRP/ha, respectively. There were no significant differences in NO3−-N leaching losses amongst the different forms of effluents. There were no significant differences in total N2O, CO2 emissions, and CH4 uptakes from the different effluents (P < 0.05). Herbage dry matter yields and N uptakes were also similar in the different effluent-treated lysimeters. Results from this research indicate that land application of the treated effluents (TE) or a mixture of TE plus clarified water (M) would result in significant environmental benefits by reducing E. coli and P leaching without increasing greenhouse gas emissions.