If I will eat its skin (apples), or pesticides and herbicides are normally used en masse on it on conventional farms (the "dirty dozen", for example). For one, it is impossible to remove all pesticide residue, and they have demonstrated human health risks. Two, the runoff from these farms poses environmental problems. Hence, I tend to buy the organic variants of these fruits and vegetables. Yep, it tends to cost more, and true, there are some loopholes in the organic certification system. I mitigate the former and eliminate the latter by doing my best to shop farmer's markets.
With respect to fish, I avoid all of the red list species - species either endangered, or subject to fishing practices that are destructive. No orange roughy or Chilean sea bass for me. Beef? If it isn't grass fed and pasture raised, forget about it. But I'm still grappling with the 800-pound gorilla in the room: is it ethical to kill and eat a living, sentient being for food when I have non-sentient alternatives?
Most of the people I know would tell me I'm worrying about something that doesn't matter. I disagree. Even the lowly species of ants, those guys you walk all over on the sidewalk each day, construct elaborate hives with ventilation shafts. Some cultivate fungus for food in their subterranean dwellings. Every meat you eat can feel pain, from fish to pigs to beef. Nevermind the entirely unethical and disgusting practices of standard factory farming, even if your meat is sustainably or "humanely" harvested, it still often suffers. They look paralyzed, both those fish are suffocating while they sit in the net on-deck. Add in the environmental costs of, for example, raising a cow, and you have quite the conundrum.
The alternative? You can get all of the essential amino acids from a vegetarian diet. I've done well on multi-week stretches without meat, even as a long distance runner. But I still get deep cravings for salmon, for that grass-fed beef burger that Lunchbox Laboratory made so well (never fear, they aren't closed, just moving to South Lake Union), for that bacon in my broccoli and red onion salad...I attribute it to my body's natural craving for meat, since we are, by adaptation, omnivores.
But we are intelligent, and we have the means to produce food that fulfills our nutritional requirements without the killing and suffering inflicted on other beings. Does that all outweigh my cravings, as an omnivore by evolution? I don't know, and I'm still trying to figure out.
But I do know you do not need to eat meat to live healthy and run well.