There were a number of pools, some have been recently found at the foot of the Temple Mount. Some were believed to heal when “an angel stirred the waters”. Others were used for ritual cleansing prior to prayer – washing the hands to the elbows, and the face prior to prayer. I don’t know precisely how many, but I would imagine that the Romans added a few to Jerusalem as well, since they were big on fountains and pools. Yes, immersion was the practice and is still recommended per the Catechism, but it is usually done as shown in early Church art: a person stood in the river, or pool, or knelt and water was poured from a clay cup or jug over the head. Generally, the full immersion of the body was not done then, since it was in public with both men and women. In fact, every Jewish village had such a pool, with flowing spring water, as men immersed for cleansing for ritual after they had become unclean – such as preparing a body for burial (including family members), women had to be cleansed after childbirth and also monthly after their “moon time”. Where were they immersed? I don’t know. But if they had that large a crowd converted, I think they would have gone to the Jordan or if there were a clean stream nearby (upstream of the city, obviously) they might have gone there. The Jordan is very likely, even with such a large group, since John had baptized many there, and the banks of the Jordan, and surrounding area would have been large enough (& outside the city and Temple jurisdiction). The 3000 would have gone in the same manner as 5000 or more followed Jesus around Galilee. Some on foot, some on donkeys. It is possible. Yes, I think immersion was often done in the early Church as it was the preferred manner of baptism, although pouring the water was permitted and acceptable when rivers were not available. I doubt they dunked them completely under.
The earliest art drawings in the Church (some done from memory of those who saw such baptisms) showed a man standing on the bank of the river, a person standing about waist deep in the river, and water being poured on their heads from a cup. In fact, the earliest artwork drawings of the Baptism of Jesus by John, shows Jesus standing about waist deep in the Jordan and John on the edge of the bank pouring water from a cup on His head. That’s likely what they did in Jerusalem – went out to the Jordan. The Jordan River also had great religious significance to the Jews, dating back to Joshua. I don’t know if they did all 3000 in one day, but they certainly could have.
I know some churches insist that ONLY immersion is acceptable, some use sprinkling. According to what I’ve read in the Church teachings, immersion is preferred, but pouring is usually used more commonly and is acceptable in Church teaching. None of the Baptismal fonts I’ve seen --(except a few in ancient churches) were large enough for an adult, or even a child to stand in one. In the Apostolic times, they preferred to use a river, stream or lake. But when none were available, they simply poured water drawn from a spring (a well) and used that, as it was considered “living” water, as wells came from underground springs.