Look at Wikipedia. All the footnotes are at the bottom of the page but linked to from the footnote number (and in turn linking back up to the referring anchor). Familiarize yourself with HTML to understand how in-page links work, if you need to.
Link to footnote:
Link from footnote back to the refering footnote number:
Have clicking the footnote link "open" a small CSS popup (not a separate window but a DIV that changes the CSS
display value from
block) on top of the text. Clicking anywere again "closes" the popup (i.e. returns the value to
You can combine option 1. and 2., as it is done on Wikipedia and some scientific online journal sites.
Put the footnotes in a side margin beside the text. This can look very beautiful, if layouted well, and looks something like the side notes or short paragraph summaries in early modern texts.
Some text editors or formatting languages like (La)TeX offer specific functions for this. Google "margin notes" and the name of your text editor.
An example with figures in the margin:
As insets, similar to in-text images. Again, most text software offers functions for this.
The following thoughts might guide you in your choice:
Footnotes at the end intrude on the reader the least and are therefore best used for information not necessary to the understanding, such as sources.
If the notes contain relevant information such as explanations of terms or examples to abstract explanations in text, they are better placed closer to the text they refer to.
Finally, there are style guides such as APA that discourage the use of footnotes and prefer inline citations instead, e.g. "(Scholes, 1983, p. 43)". In online journals these nevertheless often link to the respective entry in the bibliography which, in a one-page online article, appears at the foot of the page, effectively forming footnotes.