What you will need is either:
1) Easiest: A system with direct connections to your Pi. This is what joan describes. In this case you will use direct wires to GPIO pins on your Pi. The rotary encoder you describe has a switch and thus acts as 3 switches in total. That means 3 x 3 = 9 direct GPIO connections to your Pi. And since you got 9 switches you will need 9 pull-up resistors too.
2) A shift register IC. This allows you to expand the number of GPIO inputs your Pi can handle. The Pi's SPI bus is the normal choice here. You can use it to directly interface with such a chip. A 74HC165 shift register can read in 8 switches in parallel, and costs very little. They can be "daisy chained" together to create a huge number of inputs, all just using a single SPI bus. I2C might be possible but these are special and more expensive chips.
3) A combination of the above. If you need to read out 3 encoders with switch, then you can use 1 shift register and 1 direct GPIO.