Because of distance, most work with state and federal agencies will be by correspondence. E-mail is fine for requests for information, and for items where a fast response is needed. However, any important matter to such agencies should be in formal letter form, with reference to any informal correspondence.
Personal letters are in order, and are best if an item of personal experience with the matter can be included, perhaps with identified and dated photographs, newspaper clippings, etc. A useful goal is to get the letter on one page, but annexes are useful.
For correspondence from an organization, use letterhead paper. The substance of the letter should either have been adopted at a full open meeting, or be clearly in accord with already adopted policies; the basis should be stated. The letter should close with the expression, "We request that this letter be made part of the record (of the matter).". Be certain that there is a record of the matter and action taken in the minutes of the organization.
It is likely that correspondence will relate to one of two matters. One is comments and recommendations for wording of a new regulation or law, or a redraft. Many agencies keep a mailing list for proposed changes, and it is very worthwhile to take steps to be on the list. The second family of matters relates to proposed permits. Again, a mailing list to notify of received applications is common: however, the number of applications is so large that separating out pertinent ones is work.
To be charitable, it is likely that applications submitted to regulatory agencies are incomplete. Staffs are kept small, so they are overworked. The draft of a permit may even say that the draft is based solely on data supplied by the applicant. Because of these factors, working staff welcomes truly informative letters on the matter. In these, omissions can be flagged, missing or corrected data or at least a reference to it supplied, short and especially long term impacts set forth, or, generally, what the application should have included set forth. (Just don't be confrontational).
It must be recognized that no public agency is immune to political pressure. In fact, the senior or non-civil servants' change with each administration. Their approach and orders will reflect administration policy. If an action which is clearly against the environment in the short or long term, it is likely that a political decision has entered. Further action is not not easy, but such steps as going public, making the matter a campaign issue, appeals and suits at law can be considered, have been used, and have succeeded. Care is necessary.