Seaplanes (pontoons, flying boats or amphibious) are really interesting to fly. I recently discovered this detailed guide which explains the main procedures very well. It helped me a lot to understand their basics and to discover the correct way to handle them. It covers all main procedures (taxi/sailing, take off and landing) in different conditions too.
I didn´t know that you could sail sideways for instance, instead of trying to fight the weathervaning effect caused by wind. Guide contains many useful tips as well as technical concepts.
In case you don´t have any wind or active landing area information available, you can determine it prior to taxi. With engine idle, controls neutral and water rudders retracted, just let seaplane weathervaning into the wind by itself to determine the correct take off direction to use. After some seconds nose will point to the direction you should use.
There are still some ways to determine wind direction while being airbone to decide the best landing direction to use. Water texture, waves, foam/whitecaps, moving vegetation, smoke, dust or wind farms can help you to identify the wind conditions. They are available in game to a relevant extent. Let´s focus on the information provided by water itself, as that may be the only one available in most cases.
Water texture: ripples make water texture look darker, but only helps us to determine that there´s some wind when looking at water from a distance. However darker water textures should not be always understood as windy conditions, as they can be also produced by clouds or the angle of the sun. On the other hand sometimes there may be wind at the surface but no ripples will be visible. Texture coloration changes can be seen near the top of the following picture.
Waves and whitecaps: waves will be visible as soon as some wind exist, even if no whitecaps are produced yet. Whitecaps start to be produced and be clearly visible with winds around 10-15 kts. The white part of the wave moves following the wind direction. The next pictures show waves generated with soft wind blowing from tail to nose and whitecaps generated by strong wind blowing from beach and tail.
Wind streaks: at sea they are aligned with wind, but they don’t tell you which way wind is blowing. To determine the wind direction you need to observe the shape of the waves or whitecaps in case they exist.
Inland water bodies: at lakes, ponds or wide enough rivers the water will be calm on the side where the wind blows from and ripples will appear at the opposite side. The width of calm water area indicates the wind speed.
Sea and beaches: wind direction can be onshore (to the beach), offshore (to the sea) or cross-shore (parallel to beach). Whitecaps and waves can be clearly seen in case of onshore or offshore winds, with offshore winds producing a white spray that goes up and over the back of the breaking waves out to sea. Cross-shore winds usually deform waves making them break in several directions, so that makes harder to determine the current wind direction even if waves are still visible. However there are still some options in case we find a cross-shore wind. In the next picture, a cross-shore wind into a breakwater allows us to identify that onshore wind is blowing from sea into the beach, but it´s cross-shore for the breakwater (so following the breakwater line) and for the channel in the background as well, as both sides of the channel and breakwater reproduce waves. The higher the crosswind component the more asymmetric those waves will be when hitting the terrain on the breakwater and the channel. In the picture seaplane is pointing to wind so waves are almost symmetric on both sides but still show a small difference in the area where breakwater joins the beach.
You should always avoid strong winds as much as possible as sailing into big waves will cause skipping (seaplane will bounce) or seaplane diving into the waves, making take off and landing really difficult and even turning them into a total disaster.
The following video is a nice compilation of seaplanes take off and landing procedures. Here we can see two of the most relevant parts of the process: the usage of the step and the nose pitch.
During the start of the take off run stick is moved fully backwards to increase nose pitch. This reduces the initial contact surface with water (and therefore the drag), allowing seaplane to gain speed. As soon as seaplane accelerates the transition to the step is performed moving stick closer to neutral position. The step allows pilot to control pitch for take off as the rear part of the floats or hull will not be generating drag even when nose pitch is increased for take off, because that part is slightly above water. Once airborne there will be still some ground effect slightly above water.
Short before touchdown nose pitch is increased a bit to reduce descent rate. Take into account that you will also find some ground effect slightly above water like in the take off case. After touchdown and once speed has been reduced enough so that no lift is generated when nose pitch is increased, stick is moved fully backwards as well to generate drag with the rear part of the floats or hull, allowing pilot to stop seaplane quickly.
Touchdown shall be always performed gently. Never nosedive into water surface or seaplane nose could spin resulting in a crash. On the other hand landing too fast with too high nose pitch will generate skipping (bouncing). You should normally try to set the lowest possible speed for touchdown (close to stall speed) using the step to reduce the initial contact surface with water.
Anyway take also into account current MSFS limitations for water physics. There´s terrain short below water almost everywhere, even at deep seas, so water bodies and sea have no real and effective depth. On the other hand waves do not really lift nor sink seaplane too much but water surface still generates drag, reacts to wind and allows seaplane to sail.