Yes, your water color will depend greatly on your sky color. The angle at which you are viewing the water will also affect which direction the reflection is coming from and thus what part of the sky is being reflected. You can add color to the water itself if you want, although this is not generally realistic (unless there is suspended sediment or you're simulating underwater surfacing). Just put a Default Shader or similar into the Input of the Water Shader and adjust color in the input node.
- Oshyan