It's a little hard to make out, but what media does it have in there? Ideally you want something thats rather porous, such as lava rock - its cheap! - or a course grade sponge. This is where the majority of the bacteria will grow. While bacteria will grow in the filter wool, this is pretty much just used to remove floating matter of the water, and ideally should be changed out once it accumulates waste - or washed out - to help reduce organic matter in the tank.
For the size of the pools, as well as the amount of organic life, I do think your DIY air driven filter will work.
I'm not sure how familiar you are with fishkeeping, but I do want to stress some important things just in case:
- If you are not using established media from a - healthy - fish tank (aka, it contains bacteria), it can take a good couple of weeks for the pools to cycle. To keep that in mind, I would still do large scale waterchanges every couple of days min until any bacterial colonies have established.
- When cleaning out the filter, wash in dechlorinated water - the old water used during a water change is great for this! - and never in water that contains chlorine. Chlorine can and will kill bacteria, effectively starting your cycle back at square one. Usually the media will take on a different colouration - for example, if it is white it may turn brown/orange/grey, which is usually the sign of bacteria... That is good. You just want to remove solid waste to ensure channelling of water doesn't develop, reducing efficiency.
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