The seeds are sown, labelled and logged. Now comes the most decisive week in the whole process. More seedlings are lost in the first seven days than in all the weeks that follow combined, and almost always to the same three causes: water done wrong, heat done wrong, or the fungal disease that thrives when the first two are. Get this week right and the rest of seed starting is comparatively forgiving. So slow down and let us handle water, heat and disease deliberately.
Water: bottom is better than top
The instinct is to water seeds from above, with a can or a spray. There is a better default, and it prevents several problems at once: bottom watering. Set your cell tray or pots inside a solid tray (one without holes) and pour water into the bottom tray. The mix wicks moisture up through the drainage holes, drawing water evenly through the whole root zone from below. After twenty minutes or so, when the surface has darkened with moisture, pour off any water the mix has not taken up so the trays are not left standing in a puddle.
Bottom watering wins for three reasons. It does not disturb the seeds - top watering, especially a heavy pour, can dislodge tiny seeds, wash them into corners, or bury shallow ones too deep. It keeps the surface drier, and a drier surface is hostile to the fungal spores that cause damping-off, which love a constantly wet crust. And it draws roots downward, since the moisture is below, encouraging a deeper, stronger root system than surface watering, which coaxes roots up toward the wet top.
If you must water from the top - to settle fresh sowings or moisten the surface for light-germinating seeds sitting on top - use the gentlest possible delivery: a fine mist, or a can with a fine rose held low, or even a spoon. Never blast seeds with a stream. And whichever way you water, the target is the same: evenly moist, never waterlogged, never bone dry. Moist like a wrung-out sponge. A seed that dries out after germination has begun usually dies; a seed sitting in saturated, airless mix suffocates or rots. The whole game is the narrow band between those two failures, and bottom watering keeps you in it with the least effort.
Check moisture by lifting a tray - light means dry, heavy means wet - and by touching the surface. In a warm room under lights, small cells can dry surprisingly fast; check daily. This is the one chore of the first week you cannot skip: a single dry-out at the wrong moment ends seedlings that were otherwise perfect.
The humidity dome: helpful, then dangerous
Many trays come with a clear plastic lid, or you can drape a sheet of plastic or a bag over the tray. Before germination, this humidity dome is genuinely useful: it holds the moisture in so the surface, where the seeds sit, stays reliably damp without constant attention, and it keeps a warm, still, greenhouse-like microclimate that speeds germination. During the days between sowing and emergence, a dome earns its place.
But the dome flips from helpful to harmful the instant seedlings appear, and this timing catches people out. Once seeds have sprouted, that same warm, still, saturated air becomes a perfect incubator for damping-off fungus and for the weak, stretched growth that stagnant humidity encourages. The moment you see green - even a few seedlings up - the dome comes off, or at minimum props open for steadily increasing ventilation. Do not leave it on “to be safe.” Leaving the dome on after germination is one of the most common ways a promising tray collapses into a slimy, fallen-over ruin over a couple of days. Dome for germination; air for growth.
Heat: on for germination, off for growing
The heat mat, from the setup guide, does its job now - and only now. For warm-season crops (peppers, tomatoes, eggplant, basil), the mat under the tray holds the mix in the 70-80°F band that turns slow, patchy germination into a fast, even flush. Keep it on through germination, and keep the mix from drying out, because bottom heat accelerates evaporation and a heated tray can go dry alarmingly fast - check moisture more often when the mat is running.
Then, the same rule as the dome: when the seedlings are up, most come off the mat. Continued bottom heat on emerged seedlings drives leggy, stretched growth (the plant races upward in the warmth) and keeps drying the mix. The mat’s purpose was germination; that purpose is complete when the sprouts appear. Move the tray off the mat to grow on at normal room temperature under your lights. Cool-season crops, as before, never needed the mat at all and grow on happily in an ordinary room.
There is a rhythm here worth internalising: warmth and cover for germination; light, air and cooler growing for seedlings. The first week is largely about executing that handover at the right moment - the moment green appears.
Light the instant they emerge - no grace period
This belongs to the light guide, but it happens in the first week so it bears repeating with urgency: the second a seedling breaks the surface, it needs strong light, that day, no delay. There is no grace period where a new sprout is fine in dim conditions. Seeds germinating on a warm mat in a dim corner must move under the lights the moment they emerge, or they stretch within a day. Because different cells in a tray germinate at slightly different times, the practical move is to get the whole tray under good light as soon as the first few are up, and let the stragglers emerge into the light. A day’s delay here is a week’s worth of legginess you cannot undo.
Damping-off: the killer to prevent, not cure
Damping-off is the disease that flattens seed trays, and every beginner meets it eventually. Seedlings that looked perfect one evening are collapsed the next morning, stems pinched and rotted, thin and brown, right at the soil line - as if felled. Sometimes a fuzzy white or grey mould is visible on the surface. It is caused by soil-borne fungi that thrive in exactly the conditions careless seed starting creates: too wet, too warm, too humid, too still, too crowded. Once it takes hold in a tray it spreads fast and there is no reliable cure - affected seedlings are gone.
The entire strategy is prevention, and everything in this guide already points that way. Start in clean, sterile seed mix (not garden soil). Water from the bottom to keep the surface dry. Take the dome off at germination so air moves. Provide gentle airflow - the small fan from the setup guide, or just a cracked window and an open door - because moving air dries leaf and soil surfaces and disrupts the fungus. Do not overwater, and never leave trays standing in water. Do not sow too thickly, since crowded seedlings hold humidity against each other. If you do all of this, damping-off mostly never appears. If it does show up in a tray, remove affected seedlings immediately, back right off on water, maximise airflow, and hope to save the rest - but understand that the win was available last week, in prevention, not this week in rescue.
The first week, in one breath
Bottom water to keep things evenly moist and the surface dry. Dome on until germination, then straight off. Heat mat on for warm-crop germination, then straight off. Strong light the instant anything emerges. Gentle airflow throughout, and never waterlogged - all of it, quietly, aimed at giving seeds what they need while denying damping-off the wet, still, crowded conditions it needs. Nail this week and you will look at a tray of short, green, sturdy seedlings standing up straight, and the hardest part is behind you. What can still go wrong from here - and how to read the warning signs early - is the subject of the next guide.