Configuring two bridges and assign ethernet ports to one of bridges should ensure L2 (MAC) separation between such subnets. Hence my question: what do you mean by “but works only for IP, not MAC stuff as it seems”?
Your answer is not detailed enough to determine what works and what not. Mentioning router implies you did not pass MAC separation, but rather wrongly configured firewalls.
Describe your scenario (setup and test case) with more detail.
Using two different bridges,
One Lan on a bridge the other not on a bridge
Using one bridge but two vlans
Are some ways to avoid layer2 connectivity and thus the ROUTER can be firewalled at layer3 to block any traffic.
Having a look at your config as mkx stated will show if there are firewall issues with your setup.