How do you usually keep track of a bacterial population in the environment?

I mean, let's supose that I transform some bacteria with any polilinker, and then I leave that bacteria in the environment for several days or weeks, and then I come back and start taking samples in aquous suspensions that I later filter and make the DNA extraction, and after digesting the extracted DNA with specific restrictases I do a PCR.

If the obtained fragments match the lenght of my original polilinker I can conclude that the sample has my original bacteria. And if it's not it either doesn't have my original bacteria or my original bacteria lost the polilinker.

Is that a valid way to keep track of an introduced bacterial population? Or there are simpler and faster methods for a variety of different species?