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As one of 25 appellants of the plan, the organisation held two public meetings in Otautau and Gore recently.
Federated Farmers had appealed about 40 main points of the plan.
Two of the main areas of concern were the physiographic zones and the Manapouri Power Scheme.
One of the key comments from the commissioners in relation to the physiographic zones was they were not always sufficiently accurate at a farm scale to enable them to be used in land-use rules.
Federated Farmers life member Doug Fraser said it was the submitters and the evidence they produced that convinced the plan's hearing panel physiographics were not suitable at a farm scale.
This led on to the question of why they then chose to grandparent current farm use and prevent further dairy farms or winter grazing, given the physiographics and results from water testing, he said.
Earlier this year, Federated Farmers had made significant investment in the analysis of water quality.
''We contracted a water scientist to analyse the last five years of [water] quality data,'' Mr Fraser said.
Tom Heller was that scientist and one of his key findings was the hold-the-line approach was already being achieved.
''Not surprising the latest analysis has shown further improvements and that's testament to the effort and capital investment made by the farming community,'' Mr Fraser said.
Federated Farmers was appealing to have point three ''decision makers generally not granting resource consents for additional dairy farming of cows or additional intensive winter grazing where contaminant losses will increase as a result of the proposed activity'' removed from policies 4-12.
With the Manapouri Power Scheme, Federated Farmers' main concern was about limit setting.
Life member David Rose said they were concerned about the Waiau River, because it was only 5% of the natural flow.
''The concern is they've increased the ability for Meridian to roll over its consent and the rest of the users on the Waiau will somehow have to, with very little flow, meet any criteria around limit setting.''
In the decision plan, the scheme had gone to controlled activity, from restricted discretionary activity. This means a resource consent is needed but is always granted.
''That's what we are concerned about,'' Mr Rose said.
Looking into the matter further, the hearings panel went against the advice of Environment Southland staff who had recommended a restricted discretionary activity, and it was only a majority decision, not unanimous.
''Obviously it was very hard for them and very hard for us.''
One other concern was should the Waiau be considered over-allocated in the future, and Meridian's consent secured for the life of the plan, the burden would fall on the other water users in the catchment.
''So what we want is everybody in that catchment, the farmers, the community wastewater, everybody in that catchment to have the opportunity to have the whole community, including Meridian, involved in the limit-setting process.''
The Federated Farmers appeal requests future permits with Manapouri Scheme be considered restricted discretionary.
25 appeals on proposed Southland plan
Industry, organisation, businesses and individuals have all appealed the proposed Southland Water and Land Plan.
The Environment Court has received 25 appeals on the proposed Southland Water and Land Plan.
Appeals have come from all three councils, in a combined appeal, Federated Farmers, Beef + Lamb New Zealand, DairyNZ, Alliance, Meridian Energy, Fish and Game, Forest and Bird, Director General of Conservation, H W Richardson Group, Transpower New Zealand Ltd, Fonterra, Horticulture New Zealand, Rayonier and others.
Seven appeals have come from individuals.
Director of policy, planning and regulatory services Vin Smith said the next step of the process was a chance for people to join an appeal (called a section 274 party).
''It's likely that this step won't be complete until after June 8.''
All submitters on the plan would have received copies of the appeals.
The Environment Court registrar manages this process.
Following this, mediation is generally the court's preference for resolving appeals and the Environment Court will appoint an environment commissioner to run the mediation.
This process is confidential until such time as any agreements are reached and accepted by the Environment Court judge.
At that time the proposed plan will be amended and adopted by the council.
The proposed plan will then be operative and previous plans, like the Regional Water Plan, will be superseded.
If mediation is unsuccessful, or a party wishes to bypass mediation and go to a hearing, the appeal will be heard by the Environment Court.
Mr Smith said getting to this point in the process was a significant milestone and he wanted to thank everyone who had been involved.