When we chemically or mechanically kill this vegetation, the vegetation will decompose. this decomposing plant matter will use oxygen in the decomposition process. It will also provide food and fertility for the lower life forms, which will then reproduce at a higher rate. The consequence of this is that filamentous algae may form in larger quantities, requiring us to treat it!
The best solution to the problem, is to use only as much fertilizer as the lawn can absorb, and provide the most appropriate treatment to the pond or lake until it returns to it's natural balance.
One seemingly ironic note is, that some lakes and ponds may have excess vegetation due to low fertility. Often the best vegetation control will be to add fertility. If there is an appropriate amount of planctonic algae resulting from the addition of the fertilizer, this will color the water a uniform shade of green, lowering the amount of sunlight available to allow photosynthesis, thereby lowering the ability of plants to grow.