how can human activity affect a creek ecosystem?

the creek is located within a rural-urban catchment where rapid development has taken place. The creek itself, has experienced years of deterioration due to industrial pollution and urban run-off. It has been heavily modified in its middle sections to provide flood protection once extensive wetland areas and also in upstream tributaries.
with measurements made, there was no phosphorus or nitrate found.. in fact the water was clear, and seems "healthy".. the only human activity found were mats and garbage..

toxins/rubbish washed from stormwater into the creek, some chemicals such as phospherous breed algae which is pretty bad in excessive amounts