Have you ever thought Johns movement started for those who did not have a mikveh out in the country?
But really I think its a bit different, ritual immersion and a one time event is a bit different being those who were baptized still used a mikveh but they used it in a different way.
After all it was required to enter the temple.
Many if not most people in those days did not use constructed mikvaot. They used natural bodies of water-- springs, lakes, the ocean. Just as, for example, John apparently used the Jordan. Constructed mikvaot were a city phenomenon, for the most part, or villages with particularly wealthy patrons-- the exception, of course being the compounds of ascetic communities like Qumran. Large cisterns for mikvaot were expensive to make and maintain, and took a long time to fill. It was generally easier to use natural bodies of water.
Also, keep in mind, the majority of people did not go frequently to the Temple. Most went for the pilgrimage holidays, if they went at all, and that's only three times a year. They probably used the constructed mikvaot in Jerusalem for that, but one often had to immerse at home for other reasons, so it would have been much more usual for them to use natural mikvaot.
If I had to guess, I would imagine that Jesus-- and perhaps John-- were linking the ritual purification of mikveh with the poetic imagery in the prophets (cf. Ez. 36:25) of purification of the spirit. But the replacement entire of mikveh with a token sprinkling of water for largely symbolic spiritual purposes is unlikely to truly have roots in ritual practice of Jesus' time-- probably well after his death.