While there is no magic formula for finding the right venue for a manuscript, there are general issues applicable to everyone. Here are some things to consider when selecting a journal:
Specificity: Of course not everything can get into Science or Nature, but neither should they. Every field has an array of journals with varying specificity, and you should target a journal that fits the broad implications of your conclusions. The manuscript may best suit an ecosystem-specific journal, or a technique-specific journal. It is only when a result has larger implications beyond the confines of the study does it merit publication in broader-themed journals.
Target audience: This can be difficult when work straddles basic and applied fields, as with environmental science and ecology. Scientists in one area may not read, or even be aware, of journals intended for another area, even when topics overlap. In this case, it might be a good idea to try and publish in a variety of journals that span different target audiences. If your study has produced multiple manuscripts, spread them around. Cross-referencing journals intended for different target audiences will introduce those audiences to your work in otherwise less-read journals.
Referees: Suggesting appropriate referees is vital. Here, match your referees to the target audience of the journal. Don’t suggest referees that do not tend to publish in the journal, or similar journals, to which you are submitting. If you get a comments in the reviews like “Analysis/Interpretation – This seems ok, but I am not a modeler or a physical limnologist.”, you suggested inappropriate referees.
Reputation: Unfortunately the publication record of some journals doesn’t quite match their stated missions or scopes. So although your manuscript might match the journal “on paper”, ask around. You might find that your colleagues have experience with that journal, and know what they tend to publish and reject.
As an author, you have to trade-off shooting for the best journal possible, perhaps with a high impact factor, and the risk of a delay from being rejected and having to submit to another journal. Shooting for the stars is great, and I encourage everyone to at least try for a Science publication at least once in their careers. And take heart -nobody always hits the right journal, the first time, every time.