Well, the first thing you need to establish is whether this phenomenon of the stems is ooF (out-of-Focus) which would be a result of it being outside the DoF (Depth of Field), or whether it's due to blurring due movement of the stems (I'm assuming you turned the filters off).
Filter was left on
If it's a matter of DoF then one option is to move back for the shot. The further away from the subject you are the deeper the DoF will be. You can then crop away the area you didn't want, however the unwanted area around the tank will influence the exposure if set to automatic. It's not clear to me whether you have manual control.
Thanks for the tip, i got as close to the tank as possible, i have manual control and load of other settings:
http://www.cameras.co.uk/reviews/fuji-finepix-s5700.cfm
As Mark says, you can hold your position and stop down which also increases DoF but the penalty there will be a higher ISO and therefore noise. I'm appalled that you only have access to f6.3 and f13.6. That's about 2 stops which means to get the same exposure (and same shutter speed) you'll need ISO 800. So, you'll gain DoF but will have more noise and will loose some overall sharpness due to diffraction. It may be a good tradeoff though. What you need to du is to shoot both apertures and view both photos on your monitor at 100% zoom setting in your image program so that you can see the flaws in each.
Thanks for the info, i do have other aperture settings, i should of made that clearer (3.5, 4, 4.5, 5, 5.6, 6.3, 6.8, 13.6) It is a shame, f/9 would of been handy

I will try at ISO 800, like you say, to get the extra DoF the noise may be worth it, plus i dont know how much noise will enter at this stage as i havent tried it yet (although i am assuming a fair amount)
Remember that any half way decent image program will easily be able to recover data in an underexposed shot. Two stops is not that difficult and I do it intentionally all the time to keep the shutter speeds high and to keep DoF. Your image program is as (or more) important as your camera.
Tell me about it, i am learning new tools everyday on GIMP and all the time my photo editing skills are becoming better

I also have paint.net as it has a few different features that sometimes come in handy.
Thanks again.