Aside from the location and scenery, there are a few differences between the rivers. These include the grade of rapids, the amount of rapids rafted and the swimming ability needed by participants.
Shotover River - Is graded 3-5 (5 is the highest grade commercially rafted in the world), therefore it's a more exciting river to raft, harder to navigate and with a higher risk of falling out the boat. There are more rapids on the river, compared to the Kawarau including a section through the 170m long Oxenbridge tunnel. It is a requirement that participants be able to swim on this river.
The drive to the start of the Shotover river rafting trip is via Skippers Canyon which is an experience in itself. The narrow dirt track road hugs the sheer cliffs of the canyon and gives spectacular views over the river you will be rafting.
Kawarau River - Is usually graded 2-3 (however occasionally grade 2-4 at higher water levels), therefore easier to navigate and with less risk of falling out. There are flat stretches of river between the rapids where you'll have the opportunity to race your friends on the other rafts or jump out and swim, also watch out for the other rafts as there's always a good chance of a water fight breaking out.
The Kawarau River is a much deeper and bigger river, flowing through some spectacular Central Otago vineyards and the trip ends with a 400 meter long, grade 3/4 rapid.