There are too many possible causes to list, so I'll just relate my personal experience.

I find that I get more lower back pain if I don't use proper form while riding. If I get lazy and lock my elbows, let my hips rotate forward (i.e. arched back instead of bowed back), and fail to pedal circles then my back feels it more the next day. The negative consequences of poor form are increasing with every passing year for me (I'm soon to be 60), so I've got that going for me.

There are other factors - if I'm doing core exercises that helps with lower back pain; sleeping on a firm mattress also helps; not sitting too much (office, watching TV) helps - but proper form is the biggest factor during a ride. This is assuming a properly fitting bike, of course.