Whenever I cut acrylic (or any similar plastic sheets) I have found it is best to use a tablesaw or jigsaw first and cut to 1/8" or 1/4" oversize, and THEN use a router to make the final pass.
The less material removed with the router, the cleaner the cut will be. If at all possible you don't want to remove more than the radius of the router bit. (So, if you have a 1/2" diameter bit, then try to take 1/4" or less off with the router.)
This helps minimize "chatter" marks in the edge, heats the piece up less, and is better on the router motor and the bit, so they last longer. You also end up throwing less shavings all over the place, and you net out wasting a little less material if you can cut straight with the saw.
If a jigsaw blade only removes >1/16", and then you take another 1/4" w/router (4/16"), so only 5/16" total shavings thrown everywhere. Meanwhile, if you make a single pass with a router then you're taking 1/2" off, or in simple terms... 8/16".
You save 3/16" of material if you take 1/4" off with router, and even more saved if you can limit it to 1/8" with router, and you'll get a nicer cut.
But... keep in mind... the less you leave to take with the router, the better your first cut has to be from a straight-cut standpoint, as there is less room for error.
In a perfect world you would cut it with a huge beamsaw or pinrouter in one pass, but assuming you don't have this equipment available to you, the above stated is what most people have available as equipment for home projects, and works well.
Make sense?
(FYI: Have limited time with cuts specifically for aquariums, but was a commercial millworker/cabinetmaker for many years. Doesn't matter what the material is used for, the reaction with the tool is the same if the material is the same. I had to do a lot of plastic fabbing in my day. There's a bunch of it incorporated into cabinetry in casinos here, and they were the bulk of our work...)
ETA:
If you jigsaw first, make sure you have either some masking tape on the piece where the jigsaw is going to travel, or some on the foot of the jigsaw, or, ideally, BOTH.
The foot of most jigsaws will make nasty scratches in plastic, so you need the masking as a buffer/cushion to prevent this. And, the factory plastic cover sheet on the acrylic is too thin/soft/easily torn to be of any reliable protection.