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"Then went out to him Jerusalem, and all Judaea, and all the region round about Jordan, 6 And were baptized of him in Jordan, confessing their sins." (Matt. 3:5-6, KJV)
My question is two fold. First where is John getting the idea of water baptism from, since no one had done such a thing before him? Second in the gospel of Mark it says people were confessing thier sins, why, isn't that something only done at the temple when a sacrifice was made?
Oh, but water baptism had been done many times before! In many types of situations, for multiple different purposes. But in all cases, immersion in clean water is an act of purification.
The laws of purity and impurity are complex but chapter 16 of this book explains them well. Note, however, that this linked explanation also includes Karaite interpretations that are not in the written Torah.
John's baptism is grounded in a thorough understanding of purity and impurity as revealed in Torah and by the prophets. If you search for allusions to immersion in the prophets you will find amazing parallels.
For example, Ezekiel observed a stream of water emerging from the altar in his vision of a Temple, and out under the steps. This stream became a great river of flowing (living) water which he was immersed in as he followed it. (Ezk 47) Later, on the last day of Sukkot, Jesus stood on the steps of the Temple and proclaimed, "Anyone who believes in me may come and drink!" See the parallel? (John 7:37)
Even an exercise in looking for the first occurrence of immersion in water reveals mysteries.
Baptism itself is by no means an innovation of John the Baptist. Only his application of it was unprecedented.
As to the second part of your question, which is a good question, even the immersion performed "at" the Temple was not performed inside the Temple, but around the perimeter. The Hebrew word translated sacrifice is qorban, literally to come near or approach. Before approaching Adonai in sacrifice, the Jew was immersed to purify the body. Dozens of mikveh baths have been excavated around the Temple Mount in modern times that were used for this purpose.
John's baptism was based on the premise that confession of sins, repentance and immersion is an act of purification of both body and spirit. This is why Simon Peter at Pentecost, standing among the mikveh baths, declared that one must "repent and be baptized for the forgiveness of sins" (Acts 2). This doctrine did not begin with Yeshua, it was taught by Yochannan the Immerser. Neither the purification of the spirit through confession and repentance, nor the purification of the body through immersion, is required to be done on the Temple grounds. Yochannan ministered at the Jordan river because it is a convenient way to immerse in living water.
To prove the validity of John's baptism using only Tanakh requires a deep, clear and thorough understanding. John and his movement that waited for Messiah had this doctrine, but the Pharisees and Sadducees doubted it, which is why they sent interrogators to the river to question him.
Elisha asked Naaman to dip himself in the Jordan is a type of baptism.
2 Kings 5:9 So Naaman went with his horses and chariots and stopped at the door of Elisha’s house. 10Elisha sent a messenger to say to him, “Go, wash yourself seven times in the Jordan, and your flesh will be restored and you will be cleansed.” ...
14So he went down and dipped himself in the Jordan seven times, as the man of God had told him, and his flesh was restored and became clean like that of a young boy.
Both Elisha and John require faith from the one who is dipped in the River Jordan. Jesus himself mentions this special occasion in
Luke 4:27 And there were many in Israel with leprosy in the time of Elisha the prophet, yet not one of them was cleansed—only Naaman the Syrian.”
Did the Jews only confess their sins in the temple? No.
1 Kings 8:37 “When famine or plague comes to the land, or blight or mildew, locusts or grasshoppers, or when an enemy besieges them in any of their cities, whatever disaster or disease may come, 38and when a prayer or plea is made by anyone among your people Israel—being aware of the afflictions of their own hearts, and spreading out their hands toward this temple— 39then hear from heaven, your dwelling place. Forgive and act; deal with everyone according to all they do, since you know their hearts (for you alone know every human heart), 40so that they will fear you all the time they live in the land you gave our ancestors.
A specific example of this can be found in Daniel 6.
