The widespread problems associated with cultural eutrophication are well-known. Essentially, humans dump a lot of biotically important elements into water, and the resulting algal and bacterial dynamics render those waters pretty unfavorable for native species and desirable species (i.e., you get a lot of fish kills and stinky water).
A big source of those nutrients is agriculture. Row-crop agriculture, in particular, is a huge source of nutrients to streams and rivers (and ultimately lakes and the ocean). When people discuss these topics, they tend to focus on the raw quantities of the most important nutrients: Phosphorus and nitrogen. There's good reason for this: Typically, adding phosphorus [pdf] to lakes causes eutrophication all by itself. So it is certainly true that the quantity of nutrients added is important.
However, the ratio of nutrients that is added can also be important, particularly when nutrient inputs aren't at ridiculously high quantities. The importance of nutrient ratios in determining the function and species composition in aquatic ecosystems is an area of on-going, intense research (including some of my own). However, at the watershed scale, there haven't been a lot of studies documenting what controls the ratio of nutrients. Agriculture, of all types, typically gets treated as the same, and typically is linked to particular elements.
I've had a paper rejected recently on the watershed controls over nutrients, and one of the criticisms was that I didn't put it into the appropriate context. Well...that's a problem. So I'm taking the time to go back and re-read papers I've already read and reading for the first time some papers that I probably should have read.
One of the first ones on my list is also a relatively older paper, by Arbuckle and Downing (2001; full cite below). For whatever reason, this one didn't sink in the first time I read it. It is a note, rather than a full article, so it is shorter, but it is very good. Essentially, one of the authors, in a previous paper modeled the amount of nutrients in cow manure, and found that the N:P ratio is actually pretty low, whereas the runoff from row-crop agriculture is pretty high.
Why does it matter whether the N:P ratio is high or low? Haven't we discussed Liebig's Law? Well, we have, but I'll recap. Algae (and all life) is composed of N and P (and a bunch of other stuff) and that N & P is used in a particular ratio. So if you've got tons of N, but very little P, then you won't be able to use all the N because the amount of P is insufficient to build the proteins and so forth that you need to grow (the reverse is also true, and you can pick any two biotically relevant elements and play the same game).
We typically think of "pristine" streams and rivers and lakes as having a pretty high N:P ratio, meaning there is more N than they can use. So if you add more P, you get more growth from algae and bacteria. Hence, algal blooms (bad news!). What Arbuckle and Downing (2001) pointed out is that the ratio of nutrients coming off different agricultural systems varies tremendously. Sure, a farmer may be pouring fertilizers onto his fields, but what is in the fertilizer?
So the authors went out and measured N:P ratio in a bunch of streams and related it to the agricultural practices in the watershed.
The unusual result is that the N:P ratio of material coming off of these intensely fertilized agricultural systems has a very low N:P ratio (i.e., an N:P ratio you would expect to see in a pristine system) whereas the N:P ratio of export from intensely grazed lands will be much lower (i.e., an N:P ratio more typically associated with huge growth in algae and algal blooms).
That's a pretty counter-intuitive result. You typically look at pasture lands as being less damaging to both the terrestrial and aquatic habitats than row-crop agriculture. And maybe even here they are, but not in terms of nutrient ratios.
I think the key here is in where the study took place; Iowa. There really wasn't anywhere that the authors could go in that state without dramatic nutrient pollution in terms of sheer quantity. Most of their watersheds were greater than 50% row crops. As the authors point out "Most Iowa lakes are eutrophic or hypereutrophic..." (p 972). However, as the authors point out, the differences in nutrient ratio between the row-crop and animal agricultural systems may cause differences in the algal species that becomes dominant in a system.
I interpret this as: Well, you may get a bloom, but there's a big difference between an algal bloom and a 'harmful algal bloom'. The former acts by starving the water of oxygen when all those algal cells die. The latter actively poisons the water. Good winds or the right conditions will completely alleviate the effects of an algal blooms caused by a 'non' harmful species, but you are going to have dead fish and irritated people if you end up with Karenia brevis (one agent of the notorious red tides).
Not all agriculture is created equal, at least in terms of nutrient export.
Arbuckle, K.E., & Downing, J.A. (2001). The influence of watershed land use on lake N: P in a predominantly agricultural landscape Limnology and Oceanography, 46 (4), 970-975