You could build a series of small step dams in your stream. This way you can adjust the depth that your rocks sit in the water. The easy way to do this is to dig trenches under your liner.

Almost everyone uses the expanding foam in aerosol cans to fill the gaps under and between rocks so that water will flow over instead of between and under them. Pond stores carry it in black. However, it is the same thing that you can find in hardware stores called 'Great stuff'. GS is beige, but it soon gets covered with crud and algae and will look natural.

The stuff is horribly sticky and you will almost certainly get it on you AND your clothes. Wear your painting duds and disposable gloves (double or tripple them). The stuff Cannot be removed from clothing and will not come off later!!! The only way to get it off your skin is to wait for the skin to wear off!!

Chas suggestion of putting on more than one pair of plastic gloves is not to be ignored!!! LOL That is what I do. When the top pair gets too gunked up, I pull it off and continue on.

Expanding foam is wonderful for what you want to do. But pay attention to the word "expanding". It does just that. It is easy to get too much on in the beginning, but it does age so that it is hardly noticeable. Another thing you could do is have a pan of sand handy to sprinkle on any foam that is visable. That can blend things in.