Elemental nitrogen quickly converts to nitrate whenever oxygen is around. Rainwater and irrigation leach nitrogen and nitrates from the soil into surface and groundwaters. Excessive nitrates in drinking water can harm normal development in children and may lead to cancer in adults.
Phosphorus has been targeted as a culprit in unnatural algal blooms in surface water. Some of these algae are harmless, but others are toxic to fish and other wildlife. All choke out the native plants essential for surface water health and balance.
A key step in protecting our water resources from over-fertilization is a soil test. Most university co-operative extensions offer this service at a reasonable cost. Kits are also available, though some don't contain a full array of analyses and the accuracy may be suspect.
Not only will the test tell you how much N-P-K you need; it will also indicate how to adjust the pH. Optimum pH for nutrient uptake will significantly reduce both the amount of N-P-K required and loss of nutrients due to leaching. For an in depth discussion of the components of fertilizers see my article "What The Heck is N-P-K?"
Use only slow-release fertilizers, those containing sulfur or plastic coated urea. The better ones will incorporate at least 50% of the nitrogen content as coated urea. Read the guaranteed analysis portion of the label to determine the percent contained in the mix.
If you choose to go the all-natural route stick to greensand or seaweed, raw bonemeal, and fish emulsion for sources of potassium, phosphorus, and nitrogen respectively. All are fairly water insoluble, which means they are also slow-release.
Never irrigate right after applying fertilizer. My Dad taught me the practice of "watering in". For years I religiously followed it, in spite of being a hydrogeologist. I didn't learn better until I became a Master Gardener in my 40's. All you are doing by watering immediately is encouraging the nutrients to leach from the fertilizer.
Rather than pouring on the entire amount required in one application, use smaller doses of fertilizer employed on a more frequent basis. Lawns especially benefit from at least three applications a season. A high phosphorus start-up fertilizer in May, a slow-release high nitrogen one in July, and a balanced one in September.
When fertilizing in spring, cover the newly dressed soil with mulch. Not only does mulch keep down weeds, retain moisture, and minimize erosion, it prevents leaching of nutrients from the root zone. This keeps the nutrients where the plant can utilize them.
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