A COUPLE OF WEEKS AGO, I paid a neighbor with an excavator to dig a hole six feet deep in some fallow land behind the pond. Then, with grim resolve, my crew and I pulled a few hundred dying tomato plants from the field—some already had green fruits on them that were turning brown. We threw them into the hole and covered them with a layer of soil. It was a painful thing to do.

Before that, I was advised to destroy most of the shallots we had planted in April, and some of the onions.

Now I’m looking at the potatoes and wondering what their fate will be.

Total rainfall on our farm in the month of June was 12.1 inches. The average is around 4. One Hudson Valley weather station logged 13.66 inches, the most rain in June in more than a hundred years. It was definitely a wet month, and a chilly one.

Everyone knows that plants need water in order to grow and rain falling out of the sky is essentially free water that irrigates everything at once. So why should a farmer complain?

Ever heard of getting too much of a good thing?

Under normal growing conditions, plant roots penetrate deep into the soil (as deep as two or three feet) looking for moisture. If the upper layer of the soil is constantly wet, plants have no incentive to send roots down to prospect for water. Shallow-rooted plants have less access to nutrients and minerals, and if conditions turn dry, their roots are not well situated to capture moisture at deeper levels. Therefore, too much water can lead to weaker, malnourished plants.

Excessive and heavy rain also can result in loss of topsoil through erosion. No farmer wants to see that happen. And too much rain can cause nutrients in the topsoil, especially nitrogen and potassium, to leach down to deeper levels where they are no longer accessible to plants. But there’s another, more sinister, reason why too much rain can be trouble—the proliferation of disease. Fungal and bacterial diseases are ever present in the plant world, but they are mostly held in check by the intricate ecology of natural systems. The damage they do usually is not severe. But give them rain, day after day, week after week, and it’s an entirely different story.

The first sign that the excessive rainfall and large number of rainy days in June was causing trouble showed up in our shallots. Near the end of the month, I got a phone call from an upstate farmer with whom I had shared an order of shallot seed stock, or sets. They had been shipped down from Canada at considerable expense. He asked how my shallots were doing and told me that the leaves on his were turning black. I put the phone down and went straight out to inspect my crop and, sure enough, plants that had been growing happily a day or two earlier looked like they had just been hit with a blow torch. The tops of their leaves were shriveling, turning black, and dying. It was quite a shock.

I called my local Cooperative Extension agent, Maire Ullrich, who has an ag degree from Cornell and 20 years’ field experience, and has frequently advised me in the past. Maire deals with trouble. She maintains, with some humor, that no one ever calls her when things are going well. She came out to the farm, took one look, and said, “Downy mildew,” pointing out the grayish spore in the middle of the dark patches on the shallot leaves.

Maire then added that I had earned the distinction of having only the second case of downy mildew in alliums that she had seen in Orange County in her 20 professional years. She assumed it had reached our farm by way of the imported Canadian planting stock, especially since my farmer friend in the north was having the same problem (he later confirmed that his shallots were also afflicted with downy mildew). The damp, cool weather, Maire said, would have enabled the disease to take hold and spread on both of our farms.

I stood there, absorbing the bad news and thinking of the many days we had already invested in planting and weeding those shallots, not to mention their initial cost of over $500. Maire, meanwhile, moved away and cast her trained eye elsewhere. Before I had regained full composure, she pointed out that downy mildew already was surfacing in some nearby onions. Her advice: Get rid of both infected shallots and onions. Plow them in, without delay. Then start spraying a fungicide on all other alliums (onions, shallots, scallions, garlic) or risk losing the whole lot.

There are not many fungicides approved for organic growers; those that are don’t get high marks for effectiveness. I had no idea what to use. Maire consulted with some Cornell disease experts and, a day or two later, came up with a product called OxiDate, which is essentially a very concentrated and expensive form of hydrogen peroxide. I obtained a 5-gallon bucket of the stuff for $295. I then went out and bought a tractor-mounted boom sprayer and asked one of my workers to assemble the thing and figure out how to use it.

I began spraying all the alliums that showed no sign, or minimal sign, of disease. Meanwhile, my crew went to work cutting down and covering the several thousand row-feet of infected shallots that we had already put so much work into. Because of all the rain, the ground was too wet for plowing, so we opted to cover the diseased plants rather than incorporate them into the soil. I waited a few days on the onions and, when conditions were a little dryer, reluctantly turned them in with a rototiller.

Dealing with this sudden outbreak of disease took its toll on my (and probably my workers’) reserves of psychic capital. And it used up a lot of valuable time—time that might have been spent on other chores such as planting, weeding, mulching, trellising, and generally tending the numerous other crops we grow, many of which had not received the attention they should have, due to all the rainy days in June.

On top of this, spraying pesticides does not fall into the category of “fun” jobs. Not by a long shot. Even organically approved sprays can be dangerous—they must be used with precision and care. Too much can damage the crop; not enough may have little positive effect. The label on the jug of OxiDate warned of blindness should any of the concentrate find its way into your eyes, and death should you make the mistake of drinking it.

I donned plastic-lined overalls, Nitrile gloves, goggles and a respirator, none of which feel good on a hot day. And I kept my mouth shut.

There also was a larger concern. In addition to attacking disease, fungicides may negatively affect other organisms in the air or soil. What industrious microbe, beneficial or otherwise, wants to be doused with hydrogen peroxide while going about its business on a sunny day? As I sprayed, I worried, too, about the barn swallows flying overhead, dining, opportunistically, on the tiny fungicide-coated insects that were flushed up as the tractor and spray boom traversed the fields. Worse still, I imagined that many of these insects were destined to go into the waiting mouths of baby swallows still in their nests in the barn.

Nothing about spraying is appealing, except the hoped-for positive end result. But, what’s a farmer to do? Lose the crop he or she has already spent months working on? Lose the anticipated income? Disappoint loyal customers? I can hear them now, by the hundreds, asking why we don’t have shallots, onions, and—I can barely summon the courage to say it—garlic, at our stand this year. It’s a rare farmer, organic or otherwise, who will not, sooner or later, face tough choices like these. As it turned out, we had more tough choices coming our way. The next problem surfaced a week later, in both our potatoes and tomatoes, and it was worse.

Each of these crops had been progressing nicely. Our first planting of tomatoes had already flowered and set fruit and some 12,000 potato plants were flowering above ground and developing tubers below. I might lose most of the shallots and onions, I told myself, but a good harvest of potatoes and, especially, tomatoes would help make up for the loss. That was like counting chickens before they hatched.

While trellising tomato plants on July 1, I noticed the occasional olive-brown splotch on a few leaves—probably nothing to worry about, I thought. Tomatoes contract all manner of diseases but still manage to bear marketable fruit. In my 22 years of growing them, I’d suffered a few setbacks to be sure (early blight, blossom end rot, bacterial speck and spot) but always had a fair number of good looking and good tasting tomatoes to sell. I was eager, however, to hear Maire Ullrich’s assessment of my spraying program in the alliums, so decided to give her another call.

She came out the next day and, again, it didn’t take long for her to make a pronouncement: “You’ve got it, Keith—late blight! Sorry.” I shuddered inwardly as I remembered hearing, a day or two before, late blight referred to as the “bubonic plague of plant diseases.”

I knew, from reading and talking to other growers, that, within a week, healthy plants can become shriveled remnants of their former selves. At first, brown lesions appear on leaves and stems. Soon after, dark, leather-like spots develop on the ripening tomato fruits, making them inedible. Potato tubers that looked fine at harvest can rot in storage. Though I’d never had late blight in all my years of farming, I was aware that in wet and cool conditions it’s a disease that can spread like wildfire. And wet and cool conditions were exactly what we’d had for an entire month.

I also knew that late blight, known among the cognoscenti as Phytothphora infestans, was in the air. I’d heard reports that the dreaded Irish Potato Famine disease had been sighted on Long Island and in other parts of New York State, but somehow never imagined it would find me. It was presumed to have come into our region on infected seedlings distributed by Bonnie Plants, a huge supplier of plants, with headquarters in Alabama and greenhouse complexes in several states. The infected seedlings had shown up in many of the big box stores in the eastern U.S. Even after being told that many of them carried a deadly and highly contagious disease, these money-gobbling colossi were rushing to sell their inventory of plants to home gardeners before it was too late. The worse the plants looked, it seems, the deeper the discount customers were offered. (Late blight is strictly a disease of plants. It does not in any way affect humans.)

I could tell that Maire did not enjoy being the bearer of such bad news. In an attempt to soften the blow, she went on, “It’s not just you, Keith—late blight is showing up everywhere. I bought some plants in Lowes yesterday, to take back to our lab for testing. You wouldn’t believe how sick they looked. I almost got into a fight telling one woman not to buy a large potted tomato that was reduced from $20 to $2.50. It clearly had the blight, but the bargain price was just too much for her to resist.”

The Irish Potato Famine was no joke. Potatoes, once introduced to Ireland, soon became the staple crop of the Irish peasantry. They grew well and harvests were bountiful, until Late blight came along. Over the course of several years, starting in 1845, the disease annihilated the potato crop, resulting in the death by starvation and related causes of more than a million people. And it stimulated an enormous immigration surge to North America. The problem was exacerbated by farmers doing what they had always done: saving seed to plant the next year. The infected tubers, when replanted, just ensured another round of disease. Late blight is indigenous to Central and South America, the home of potatoes. The outbreak in Ireland was probably caused by infected tubers coming up from Mexico, crossing the US, then making their way to Ireland, by boat, from New York. In the cool, damp Irish weather, the disease exploded.

“Don’t plant any of these spuds next year”, was Maire’s first utterance of advice, “even if they look okay.” She suggested that I spray all the tomatoes and potatoes with a copper-based fungicide as soon as possible. I groaned, knowing from very recent experience how onerous a task this would be. She then added that, if I didn’t want to spray, I might try going to church on Sunday and putting $20 in the collection box. I couldn’t tell whether she was serious about this. But, since I seldom find myself in a church, except for the occasional wedding or funeral, it didn’t seem like much of a plan. Which left me with copper.

As Maire’s car disappeared up the driveway, I got on the phone to see what I could find. It was the afternoon of July 3, and most companies selling agricultural pesticides were closed. I did, however, manage to place an order for a 20-pound bag of something called NuCop 50, one of the few copper fungicides permitted under organic standards. But I wouldn’t be able to get hold of it until Monday, at the earliest. There was nothing more I could do.

I tried, with little success, to expunge all thoughts of blight from my mind, and went on to harvest mint, snow peas and wild mulberries for the Saturday market. With all the rain we’d been getting, at least there was a veritable forest of good-looking mint to cut from.

As expected, the July 4 market at Union Square was slow. That meant there was plenty of time to chat. Early on, a fellow organic farmer and friend stopped by to do just that. When I told him that we had late blight on the farm he threw up his hands and said, “You’ve got to spray with copper. Now.” I told him I couldn’t get any ’til Monday. He said that might be too late and described the devastating losses he had suffered to the disease some years before. Generous man that he is, he offered to give me a couple of pounds of copper fungicide if I could find someone to make the trip to his farm to pick it up. A few phone calls later, an arrangement was made. One of my workers, Joshua, was willing, on his day off, to drive two-and-a-half hours north to obtain an emergency supply of copper. The next day we started spraying the potatoes.

We’re now in the third week of July and the weather is stabilizing. It’s still surprisingly cool for mid-summer, but the rain has eased off a bit. Over the past two weeks, I’ve become a regular nozzle-head, spending about a quarter of my time either mixing fungicides, riding on a spray tractor or, worst of all, walking through the fields with a long hose and a spray gun. I don’t know what good it’s doing. The downy mildew has moved from its place of origin to a more distant patch of onions. The stressed plants are at least beginning to form little bulbs and it looks like we might have something to harvest. A couple of small plantings of scallions bit the dust pretty hard, but so far, our garlic seems to have resisted the disease. For this I am grateful.

Latest news reports warn that late blight is now well established up and down the eastern seaboard and has moved inland as far as West Virginia and Ohio. It has definitely spread through our first planting of tomatoes, despite the application of copper. It’s just a matter of time before more plants end up in the big hole.

This year, we planted a total of 2,300 tomato seedlings in three different locations, a few weeks apart. All of them were started in our own greenhouse. The second planting is looking better. It has patches of blight but some plants show no sign of disease and seem to be growing well enough. Maybe the copper is doing its job. I’m sure the drier weather has worked in our favor but worry what will happen when its starts to rain again. It’s too soon to predict how the third planting will turn out.

Most of our potatoes now have some degree of late blight, but the combination of dry weather and copper seems to be holding the disease in check. The plants are large so have good reserves of stored energy to form their tubers. If we can just keep them alive for another two or three weeks, I think we’ll have potatoes to sell. Last night, a farmer friend and fellow garlic grower from the north country told me that I should consider mowing all the above-ground growth off the potatoes within a week or two because the late blight pathogen needs living tissue to survive. He said that if I let the tops dry out or decompose and then wait a couple of weeks before digging, there’s a fair chance that most of the tubers underground will be fine, though small. I hope he’s right.

We ended our conversation on a hopeful note, reflecting that so much adversity might lead to more empathy for others, especially other farmers, many of whom are in the same boat I’m in, or worse. And, who knows, it might even lead to a little personal character building. That would be a nice silver lining.