In the past, I have read many journal articles that describe research that happened several years before the paper was published. It used to make me wonder, what was the delay? Why did it take so long to go from collection to publication. As I go through my journey toward a PhD, I can finally say that I understand. There are many steps in the process. I'll try to walk you through them.
(1) Learn what you know and what you don't. There is no point in doing scientific research on a topic until you've figured out what has been done. Along the way, make note of things that maybe should have been done differently and thoughts on other questions that the prior studies bring to mind. These will be the basis for finding the niche of your work. As I get further in my career, I expect that this will take less time, unless the direction of the research takes a big turn.
(3) Processing samples can take a lot of time. Scientific knowledge is generally gained not one sample or site at a time, but hundreds of samples from dozens of sites at a time. Depending on the methods and equipment available, determining how much of a certain chemical is in a water sample can take several minutes per sample. So if you have 90 samples and are testing for 4 parameters that take about 5 minutes each, you are looking at about 30 hours of work, not including running controls, cleaning glassware, ensuring proper waste disposal, etc. In my experience, the most convincing studies have far more samples than this.
I am currently focused on sorting invertebrates from sediments in a set of samples collected using a Hess sampler. This process can take between from 2 to 20 hours per sample. Part of me wishes I had been tracking this so I could tell you how many hours have been spent on sorting, but I think I'm better off without this knowledge. Identifying the individual invertebrates to genus or species will take many more hours. Multiply these many hours by the number of sites and samples and invertebrates needed to reach an acceptable sample size and this can result in thousands of hours of work.
(4) Quality number crunching is vital for successful science. You know how I posted about the bajillion hours it takes to process the data needed for most good science? Well, nobody wants to look at all of that data until it is pared down to a few highly relevant numbers and a couple of figures and tables. Statistical analyses fit in here, too. Properly summarizing data into these smaller pieces is really a work of art when done well. When done poorly, it is a horror to behold. It takes time to reach the artistic stage and I don't claim to be there yet, but I think I'm beyond the nightmare stage.
(5) Writing is a process that is not for the faint of heart. There are many wonderful articles, blogs, Tweets, and other bits of wisdom that can be found on the internet or in your favorite bookstore about writing. There are strategies for making yourself start writing, for taking breaks when writing, and for knowing when its time to just stop writing. I don't feel the need to go into that here, because everyone writes differently and plenty of other people can provide far better insights than I.
(6) Still not done! So, you've written a manuscript chock full of references to the latest research, well-executed field collection and lab analysis, and artful statistics and figures. Says you... Now it is time to send it for review. Even on the most excellent papers, this process can add months to the time before publication. The editor must get the manuscript to reviewers. The reviewers must find time in their busy schedules to read and comment on the manuscript, the comments are compiled, and (unless the work is outright rejected) it is all placed back into the hands of the author for minor or major revisions. I've heard rumors of manuscripts being accepted the first time with no changes, but I have trouble believing that...
So, the process of taking a project from idea to publication can be lengthy. If this is the only thing a researcher has on their plate, then they are fortunate. Most researchers are balancing this process with teaching, networking, mentoring, grant-writing, collaborating, learning, presenting, doing other research, and (hopefully) living a life outside of their discipline. I am glad that I've been learning to juggle!