Water is one of those elements that can be tricky to create, whether you're doing a 2D texture in Photoshop, or a 3D model in a modeling program. It's easy to use some noise, add random waves, and color everything with a semi-transparent blue, but it never looks quite right. That's because water and waves in particular have so many attributes interacting, that each of these things must be incorporated in the water you're trying to create for it to look real. Here's a list of the things you need to keep in mind when creating your water.
First, the waves themselves can be tricky to make. Even during calm weather, there's always a certain amount of waves going on. Also, while using a noise filter is a good start to get waves, the fact is real waves aren't random. They flow in a specific direction, typically in a 30 degree angle arc in the direction of the wind.
Worse, each wave interacts with the others, which makes them even more complex. The best way to make realistic waves is if you have access to a physics system to make them. Otherwise, even making the bump texture by hand will often give you a better result than noise. Check out this animation
to learn how waves interact.
White caps and wakes
Waves also have a white part, called the white cap. This will be fully visible when the wave is strong enough, but even on a fairly calm sea there's still some white caps produced whenever a wave is impacted by something, like another wave, or the wake of a boat. Wakes are typically much stronger than the surrounding water, which is why their effects are much more pronounced.
Specularity and reflection
Water usually has a very high level of highlight, with the sun or other lights causing a very visible effect. Reflection must also be taken into effect, which is mostly visible near the shore or other objects. Normal water is translucent, because of pollution and other substances, which means everything in water will be color tinted. However, pure water is transparent.
Typically, you can see through water only until a certain depth. This, along with the factors above, make shore lines especially hard to create. It's important to consider reflection, translucency, and the ripple effects of the shore line when making your water. Here's an example of a water texture that shows how color can change based on the depth:
Overall, doing realistic water is one of those tasks you want to get right in computer graphics, because it's used in so many projects. It can be challenging, but by keeping those facts in mind, you can improve the look of your textures dramatically.