I have grown this pine bonsai from a seed and it has been happily growing for 3 years now. Over the past week or so the needles have been starting to close up and the plant itself smells, not the soil or roots underneath. I originally thought I hadn't been watering it enough as i have been a bit out of routine with watering, however everything i am seeing online says the most common issue is overwatering. I have recently moved it slightly away from the window but it hasn't been plunged into darkness so I don't see how that could be the cause. I have scratched the bark and it is still green inside but i fear it won’t stay that way for long unless i figure out what it needs! Any suggestions hugely appreciate.

Do you keep it indoors? Perhaps find out what species this is and read about the species care - likely you will read it should not be kept indoors

Too much water, not overwatering is mainly a problem with poor drainage. If the plant has been outside where it must be then you would not have been watering as the rain and lower temperature will have been enough, but if the soil is poor and not draining then it can be an issue. Does the soil drain well? if not then you could re pot to correct the problem. It will need protecting from frost for a few weeks, so in a greenhouse or shed. If it is draining then possibly not enough water is the cause, but only you can sort this issue. Check to see if the soil is wet, and draining. If you have had it inside then that is the problem. It must be outside all year, if you get severe frosts then protection in a greenhouse or shed is needed, not in a house.

I guess aleppo pine (pinus halapensis).

The root cause of bad health is indoor keeping. Yes, they are sensitive to overwatering. But that is really a side track in your case. You made a subtropical pine survive in livingroom conditions for 3 years. That is very impressive and do not suggest there has been any other flaw in your care except for indoor keeping.  

Jeff wrote:
"If the plant has been outside where it must be then you would not have been watering as the rain and lower temperature will have been enough."

That is information based on UK conditions. If you are anywhere else in the world you make need to take that advice with a grain of salt.

Tropfrog wrote:

Jeff wrote:
"If the plant has been outside where it must be then you would not have been watering as the rain and lower temperature will have been enough."

That is information based on UK conditions. If you are anywhere else in the world you make need to take that advice with a grain of salt.

In more detail, you need to match the tree's environment to the environment where it evolved. Most trees evolved with a definite cold period. Some areas have a winter of a month or so, some several months. Almost no living room can supply a cold enough period long enough. 

Most trees will survive over a year inside. Three years is pretty long. If you are in the northern hemisphere in a place where temperarures drop below freezing I would advise moving it to a frost free room, like an unheated garage, for now, and then outside when it warms up. Then leave it out. 

Look up where the tree evolved and match winter care to that area. I would guess Aleppo means it comes from Syria,  but that is just a guess.