If you want to get the effect without photoshop trickery there are couple of factors to think about. Generally reflections off of medium boundary (like water) are governed by Frensell equations that predict that the amount of reflected light is dependent on the orientation of the reflective surface and the polarization of the incoming light.
- The effect of the angle of incidence
When photographing water some light is always reflected, but the amount of reflected light is very low below the Brewster angle (53 degrees) and rises quite rapidly above that. What this translates to is that water photographed from above at no more than a 45 degree angle from shooting vertically will have much less reflections. So get up on a high vantage point and shoot down.
Secondly when the water is still it will keep a consistent angle of water toward the camera, a smaller angle (shooting more at a downward angle) is needed for a wavy sea than a still lake.
- The effect of polarization
Light polarized at different angles to the plane of incidence reflects in different proportions, generally all light reflects at the same rate when shooting vertically, and then one polarization decreases with increasing angle, until it is not reflected at all at the Brewster angle, after which it starts to be reflected again. Light from the sky is also polarized, most highly at a 90 degree angle from the sun, which affects the amount of reflecting sky at different angles towards the sun.
The first consequence is that a polarizing filter can partially cut out one polarization from the reflection, leaving you with less reflected light, especially at moderate reflection angles and at 90 degree angles relative to the sun (so something like mid-late afternoon and shooting with the sun to the side is usually good enough). This is widely used to get clear shots of people through the front or side windows and decrease the amount of reflected light off of a water surface. Though it will generally not eliminate all reflections, if done correctly they will be imperceptible.
The second consequence is that usually clouds will usually be reflected more than the sky (because they scatter light without polarizing it), and a polarizing filter enhances this effect, so shooting during a cloudless day will give less reflections.
The last thing to note is that it is easier to achieve all this with longer focal lengths, and positioning the frame in landscape orientation because the angle of incidence to the water will change less across the frame (this can be quite a big factor as if you were to position a typical phone camera in portrait mode the difference in the angle across the frame would be 54 degrees, so typically you go from almost no reflections at the bottom of the frame to a lot of reflections at the top).