Deb, Everything you do to a pond has pros and cons (downsides). To be fully aware of them, One has to be knowledgable enough to understand the implications of action and reaction of the aquatic communities (pond ecosystem,) to the "stimulus or stimuli".
Fertilization can be in the form of natural or artificial; organics vs inorganics. Everything natural or manmade when it is added naturally (wind or runoff) or added by humans to a pond filled with "clean" water or if in pristine condition is some form of pollution to that pond. It is a matter of degree.
Everything organic breaks down into the basic chemicals (elements) thus technically most everything added to a pond is / are chemicals in one form or another. Their environmental impact in regards to "fish ponds" basically depends what the goals are for the pond. Here we frequently talk about the importance of goals of the pond owner.
The basic chemical compositon of inorganic fertilizers is various compounds consisting primarily of nitrogen, phosphorus, and potash. Sometimes other additives for the various macro and micro nutrients are present.
If you have time, I suggest that you review many of the posts in the forum heading of - Fertilizer. If you read all of them you will no doubt be dizzy trying to assimilate all of the information.
Since you work at the hatchery, I am sure that "Ken and company" have heavily indoctrinated you, and understandably so, with their philosophies of pond management. This web site will often present both sides of many pond situations, and when viewed and studied with an open mind, they will maybe broaden your outlook and understanding about various types & methods of pond management.
In reference to your question regarding the impacts of adding inorganic fertilizer and for example; the "feed and dye method" and associated stocking rates recommended by "Kens" puts tremendous impacts upon an enclosed or contained aquatic system. In just one aspect alone, consider the amount of high nutrient manure that all those fish daily produce in a pond with no flusher. Something has to happen to all that continual manure accumulation while the artificial dye is inhibiting natural photosynthetic, heterotrophic, and bacterial processes; something has to be dramatically impacted in the whole process.
