Your title asks one question and the text of your post asks another. To help with either one, we would need to see an example of your data to understand how it is laid out. Some guidance on how to show data can be found here:
It may then be fairly easy to answer your question "how to create a boxplot with physicochemical variables?"
Your other question, "What I want is to know how to associate the presence of these microorganisms with the physicochemical variables", might be too broad to answer completely. If you can show a sample of both the physiochemical values and the microorganism data, and explain to what extent you want to associate them, someone may be able to provide some guidance. If you just want to make graphs of, say, dissolved oxygen versus the density of each organism, that might be straightforward. If you want to develop a model of many physiochemical variables predicting organism presence, that is probably more than can be done on a forum, though people will be able to point you towards literature from which you can learn how to do that.