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difference between environment variables and System properties

iam using the below link to understand environment variables and system properties.
https://docs.oracle.com/javase/tutorial/essential/environment/env.html
The link says environment variables are set by OS and passed to applications.
When i fetch environment variables using System.getenv() it shows me lot of properties which i never set.
So it must be OS (im using macOS) which had set these properties.
Some of the properties in System.getenv() are MAVEN_CMD_LINE_ARGS, JAVA_MAIN_CLASS_1420, JAVA_MAIN_CLASS_1430.
My question is why would OS would like to set the java specific properties in environment variables? Ideally these should be set by JVM (in System.properties()).
P.S.: From whatever i have read on net i understand that environment variables are set by OS and System.properties() are set by JVM
Also if someone can point me to a good link on environment variable and System.properties it will be very helpful. Iam very confused between the two.

Environment variables is an OS concept, and are passed by the program that starts your Java program.
That is usually the OS, e.g. double-click in an explorer window or running command in a command prompt, so you get the OS-managed list of environment variables.
If another program starts your Java program1, e.g. an IDE (Eclipse, IntelliJ, NetBeans, ...) or a build tool (Maven, Groovy, ...), it can modify the list of environment variables, usually by adding more. E.g. the environment variable named MAVEN_CMD_LINE_ARGS would tend to indicate that you might be running your program with Maven.
In a running Java program, the list of environment variables cannot be modified.
System properties is a Java concept. The JVM will automatically assign a lot of
system properties on startup.
You can add/override the values on startup by using the -D command-line argument.
In a running Java program, the list of system properties can be modified by the program itself, though that is generally a bad idea.
1) For reference, if a Java program wants to start another Java program, it will generally use a ProcessBuilder to set that up. The environment variables of the new Java process will by default be the same as the current Java program, but can be modified for the new Java program by calling the environment() method of the builder.

Is it possible to "fool" java that an environment variable is set from the command line

I'm running in an environment where I can pass parameters but not set environment variables using a normal commandline.
I would like to set environment variables nevertheless. Is there an alternative way to "fool" java that an environment variable is set, e.g. using -D parameters?
(I'm running spark in oozie through hue; all in the Cloudera stack).

The java command itself doesn't seem to allow that. It has a -D parameter, but that sets Java 'system properties':
$ java -help 2>&1 | grep -A1 '\-D'
-D<name>=<value>
set a system property
Java system properties are a sort of Java properties. Like environment variables, java properties are key-value pairs, but aren't the same thing as environment variables: If your Java application reacts to a specific environment variable, setting a system property of the same name won't have any effect unless the application explicitly reacts to that property, too.
If your environment allows you to run arbitrary Java applications and if it allows your Java applications to execute other processes, you can write a little wrapper that sets the environment variables on a ProcessBuilder (see the question Arnon linked in his comment: How do I set environment variables from Java?) to then invoke java with your actual JAR from it. You could either hard-code the environment variables to set, or set them according to system properties the wrapper receives. (Or you could even implement your own shell in Java and pass a script to it.)
Though, if you can modify the source of that actual JAR, a much more idiomatic solution would be to make it itself react to properties instead of (or additionally to) environment variables. (Unless you have to control environment variables that the java command / the JVM reacts to rather than the JAR you'd like to run. Then this approach would not be applicable, of course.)

If you can run arbitrary Java code, you can create and run a Process using ProcessBuilder, including an environment of your choice.
Hence, write a java program that parses a command-line like
java -cp .... your.Prog FOO=BAR BAZ=BOOM command arguments ...
and starts command with the environment extended by FOO and BAZ
(Note that command could be java ...)

Setting Shell Environment Variables from Within a Process from Java on Linux

If I had a java application that needed specific environment variables to be set, but I cannot place them inside the bash.rc or bash_profile, nor can I place them in /etc/profile.d is it possible to have them set within the Java process? Or do these need to be set before the java process is run? Also manually setting them each time is not an option because I want them to be transparent to the user.

Start the java process from a shell script. The script would first define and export the environment variables.

I suspect this is not possible. System.getenv() is an unmodifiable map, meaning you can't modify elements in it.

Environment Variables
And for setting environment variables, ProcessBuilder

Have you try ?
System.setProperty("KEY", "VALUE");

Adding environment variables using java program and able to see when I open environment tab from My Computer

I want to write java program which adds environment variables and when I open environment tab from MyComputer,then I should be able to see that...
This is what I have tried,but it gives java.lang.unsupportedexception
Map env = System.getenv();
env.put("abc", "pqr");
And One more try is below,it is not giving any error...But I can not see any value added when I open environment variables tablenter code here from My Computer.But When i sysout "env" variable it gives me all paths including myone also...But I need same thing to be shwon in environment variables tab...
ProcessBuilder processBuilder = new ProcessBuilder("cmd.exe","/c","set");
Map env = processBuilder.environment();
env.put("abc", "pqr");
Please help me guys...Thanks in Advance...

There are two ways. The first one is to call the Windows API to change/set the environment variable. You must look for the right Windows API function and call it from Java. However calling any Windows API from Java is a topic on its own.
The second way is to call the setx.exe program with the correct arguments to set environment variables. Check the manual of the setx.exe program how to use it (and when it is installed) to set your environment variables.
In both ways you obviously restrict your Java program to run on Windows systems only.

Access shell environment variables in Java

Does anyone know how to access the environment variables of the standard shell environment in Java? I am using the ProcessBuilder class and I have to specify specific environment variables used in a shell script I am running, these variables exist in the standard shell environment.
Accessing ProcessBuilder environment does not work.

You can get at the environment variables that existed when your program was created through System.getenv():
http://download.oracle.com/javase/tutorial/essential/environment/env.html
When a Java application uses a ProcessBuilder object to create a new process, the default set of environment variables passed to the new process is the same set provided to the application's virtual machine process. The application can change this set using ProcessBuilder.environment.
It looks like your child process should get your environment automatically.

processBuilder.environment().get("variablename");