If it about impact on water quality, benthos can be used as indicators. Members of chironomidae family viz., Cricotopus, Dicrotendipes are known to be associated with agricultural inputs.
Can you narrow down your question?. Indicators could be ecological (as Abhilasha Bhawsar has answered). But it may be you wanted to ask "What are the observable and quantifiable parameters/indicators which show that Agric intensification is taking/has taken place?"...and in this case, i could say..