Then, what happens afterwards depends on the flow rate of the water, the soil composition, the geometry of the landscape, and so on:
1) If there's significant seeping into the ground: the land around the lake becomes muddy. The water table may rise. Crocodiles may move into this new mudhole. The lakewater becomes murky, because the constant high flow is causing currents and turbulence throughout the lake, especially near the rune. Because of the higher water tables, other nearby places also become saturated with worst-case scenario: water, creating mud, swamps, flooding, and structural damage. More wetlands form. There are more places for mosquitoes to breed.
2) If there's significant evaporation: The air around the lake becomes more humid and it may rain more. This may cause more erosion in places that wouldn't have it normally. May cause occasional flash flooding if there's really thin valleys downwind. Plants will grow around the lake. Crocodiles or other animals may move in. There are more places for mosquitoes to breed.
3) If evaporation and ground seepage aren't enough to prevent water from forming rivers leaving the lake: A river will suddenly form, and several streams may form. Steady-state, it will have approximately the same flow rate as the rune. This will, initially, cause flooding downriver, and a lot of erosion as the water cascades downwards. Sandbanks will erode away and build up, and in the immediate future the river will likely change course several times until the erosion eventually slows. More plants will grow around the river. Crocodiles may decide to move in.
There will also be societal and economic effects. If the new lake can remain unaffected by contamination from the soil, parasites, and mosquitoes, it will make the people around it healthier. More plants (including fruit trees) will be grown in the areas around it. If it can remain free from corporations, it will be a great boon to the society. The new flooding, erosion, rivers, and wetlands will change what crops can be grown, what pathway you take to walk to religious services or work or friends' houses, and so on.
Plus, the sudden appearance of several lakes will immediately gather the attention of world news organizations, governments, and religious leaders. They will show up all over the news, and scientists will investigate them. Eventually, once they find a way around the crocodiles, they'll discover the runes on the lake floor.
Then, magic will be revealed to the non-wizarding world. The African wizards and witches will probably be pressured to reveal themselves. The North American Scourers will expand their influence across the world, especially to Africa, and begin public witch hunts. The wizarding community will declare open war on the witch-hunters. Magical attacks will be blamed on new bioweapons in the news, and positive relationships between nonmagical governments and magical governments will shatter. Wizarding governments will fracture. The source of the lake will eventually be traced back to Harry Potter and Hogwarts. Great Britain will be further isolated from the rest of the wizarding community, while Scourers attack everywhere else. Magical communities will blame the Great Britain wizards for these attacks. New groups similar to or worse than the Death Eaters will crop up. Due to decreased unity, magical beasts all over the world will be no longer hidden as well, will be spotted, and the wizards won't be capable of covering up their existence much longer. Great Britain wizards will be under attack by Scourers, Neo-Death Eaters, foreign wizards, and non-magical governments. J.K. Rowling will be forced to write a new Harry Potter universe movie that takes place in the post-Harry Potter apocalyptic future.
Crocodiles may take up residence.