hey there HL, make the tray lightproof without light algae cannot grow, changing the water will not prevent algae their spores will grow as long as theres water and light, however changing the water regularly will help rooting and will keep the water low in bacteria larvae and dirt, i use low dose H2O2 in my cloner keeps things clean. never had trouble cleaning it, is your tray smooth surfaced like all plastic trays around? never heard of hard to clean algae on smoothe plastic, i guess you let tray dry up with algae in it that would make it harder to clean, still you can use some bleach and water rub a bit it should get off easy