Let's make one thing clear: Working in a messy, disorganised space is a recipe for disaster. Not that it is uncommon. Lots of students tend to work in spaces that are not entirely fit for purpose.
That is why having a clean, organised work space is so important. There are a lot of things related to study / productivity that we can't necessarily control. However, the space in which we work is one thing that we absolutely can control.
First off: De-clutter! The trick here is minimalism. Get rid of absolutely everything that is not related to your work. Cleanse your desk / workspace of all the unnecessary items that are simply taking up space. Find a new home for those cactus plants.
Get filing: This one is so important. Take the time to establish a clear and organised filing system for all of your study notes. You can buy reasonably cheap folders in most stationary shops. Organise your files / notes by subject or even by topic (if you are really committed to organisation). While this is definitely a long, boring process, it will save you so much time in the future.
Storage: You don't need to spent a ton of money, just be wise with your stationary purchases. Buy a cheap jar to store your pens/pencils (or even just use a mug in your house). There is nothing worse than trying to work in a space that is littered with pens, pencils and other stationary items. Find somewhere to store these - so that they are easily accessible and are not getting in your way. You can also buy mini shelves (again, it won't break the bank) to store your notes and organise your folders.
Benefits: Research has shown the benefits of having an organised and tidy workspace, that is conducive to study. Such benefits include: improved mood, less likely to feel anxious/depressed, less likely to become lazy/lethargic, and overall an increased likelihood of being productive, agreeable and positive.