We perform comprehensive studies on the fundamental loss mechanisms in III-nitride waveguides in the visible spectral region. Theoretical analysis shows that free carrier loss dominates for GaN under low photon power injection. When optical power increases, the two photon absorption loss becomes important and eventually dominates when photon energy above half-bandgap of GaN. When the dimensions of the waveguides reduce, the sidewall scattering loss will start to dominate. To verify the theoretical results, a high performance GaN-on-sapphire waveguide was fabricated and characterized. Experimental results are consistent with the theoretical findings, showing that under high power injection the optical loss changed significantly for GaN waveguides. A low optical loss ~2 dB/cm was achieved on the GaN waveguide, which is the lowest value ever reported for the visible spectral range. The results and fabrication processes developed in this work pave the way for the development of III-nitride integrated photonics in the visible and potentially ultraviolet spectral range for nonlinear optics and quantum photonics applications.