Aside from one occasion when I accidentally landed right next to a patch of it, all of my bacteria discoveries have been made by listening for the characteristic echo of the hand scanner ping. One or two were near a local ridge and so I was able to see the edge of the green afterglow, but the rest were out of line-of-sight and have required a bit of movement and continuous pinging to locate. I feel sorry for anyone with hearing difficulties trying to play this aspect of Odyssey. The sound of the echo is absolutely critical.
One thing that may be obvious to a lot of players but caught me out for a while; the scanner ping is omnidirectional. The green wave radiating out gives the impression -- at least on my 21:9 monitor -- that it's radiating in a fan-shaped pattern in the direction the scanner is pointing, but that's just a visual artefact. If you have head-tracking or free-look you can confirm this by looking to the side when you ping, and you'll see the same pattern radiating in all directions. For a long time I was wasting time standing in place and pinging all four cardinal directions to cover all of the area, but it's not necessary. If you're hearing an echo but can't seem to zone in on it, it's probably behind you.
The SRV scanner will highlight patches of bacteria, among other things, by strobing the reticle as it passes over them. Because SRV scanners appear to have a wider arc at longer distances, and work through the ground, it's possible to detect patches this way by driving at reasonable speed over undulating terrain and looking for strobing as the nose of the SRV dips. If you want to combine bacteria hunting with general surface exploration this can be an efficient way of doing it. On smoother ground an alternative is to start the SRV moving slowly, then switch to the turret and manually sweep the scanner around the local area looking for strobing. Depending on how your controls are set up you may still have limited control over the SRV itself while doing this; with mine I can control the throttle and thrusters but not steering, so I can hop over problematic rocks or bring the SRV to a stop if it approaches dangerous terrain.
Finding that elusive third sample on a bacteria-only world can be quite rewarding but it's a slow, zen-like process. If you're in a hurry to get somewhere else, and are not a completionist, it may not be worth the frustration. If you're not enjoying the ride, the destination probably isn't worth it.
I'm hoping at some point that FD introduce missions geared around biological scanning. If I was told to fly to a specific planet and bring back data on all of its organics, it would feel more important to me even if the credit rewards weren't fantastic. Maybe some of the new Engineers unlock in this way? It's not something I've looked into yet.