use a plastic/fiberglass window screen on the intake and or the outlet ,,,,, remember bigger is better, so its a long time between cleaning.
Now if you water smell bad its a another porblem, bugs, alge, etc.
You might want to bleach you system out, and use a little hydrogenpoxide to kill the smeller grower.
I have large tanks and never had that problem.
You might want to say clean the living shit out of you tanks and system.