Brown, soft or sunken stem base or crown

Likely causes, most likely first

Ranked for this sign on its own. Your stage, medium and readings change the order, so run the checker for your plant.

1. PossibleFusarium wilt or crown rot

   DiseaseAct within a day or twoRead: Fusarium in cannabis: wilt, crown rot and bud rot

   Fix: No cure once infected: remove the plant with its medium in a bag, sanitise pots, trays and water lines, and use clean clones and new media. Reduce root stress (overwatering, heat, salts) on the rest.

   Recovery: No further wilting plants over the next 2-3 weeks.

   How to confirm it

   • Cut a wilting stem lengthwise. On a wilting or dying branch, scrape the lower stem and cut it lengthwise with a clean blade. Brown streaks in the water-conducting tissue point to vascular wilt (Fusarium). A dark, sunken crown points to crown rot. Disinfect the blade afterwards.
   • Send a sample to a plant diagnostic lab. For rots, wilts, leaf spots and viruses you can't separate by eye, send a fresh sample (whole plant with roots or a wilting branch with healthy and diseased tissue) in a sealed bag to a university or commercial plant diagnostic clinic. Results in days to 2 weeks.
   • Look at the roots. Hydro: lift the net pot and look at the root mass in good white light. Containers: tip the plant out with a hand over the medium and look at the edges and bottom of the root ball. Healthy roots are white to cream with fine fuzzy tips. Brown roots whose outer layer slides off between the fingers leave a bare thread: rot. Firm, evenly tan roots with white tips in coloured solution are staining.

2. Less likelyRoot rot (Pythium)

   DiseaseAct nowRead: Root rot and Pythium in cannabis

   Fix: Act now. Fix conditions first: solution at 18-21 °C (65-70 °F), strong aeration (6-8+ mg/L DO), no overwatering. Change the reservoir, trim dead roots with clean scissors, clean and disinfect the system. Then either re-establish beneficial microbes (Bacillus, Trichoderma; house-preferred) or commit fully to a sterile regime (e.g. dosed hypochlorous acid or peroxide). Isolate affected plants on recirculating systems.

   Recovery: New white root tips within 3-7 days and wilting stops; brown roots don't recover.

   How to confirm it

   • Look at the roots. Hydro: lift the net pot and look at the root mass in good white light. Containers: tip the plant out with a hand over the medium and look at the edges and bottom of the root ball. Healthy roots are white to cream with fine fuzzy tips. Brown roots whose outer layer slides off between the fingers leave a bare thread: rot. Firm, evenly tan roots with white tips in coloured solution are staining.
   • Smell test of roots, medium and reservoir. Smell the roots, the bottom of the root ball, the drain water or the reservoir up close. Healthy roots smell earthy or of nothing. A sour, rotten, swampy or sewage smell means anaerobic conditions and rot. In hydro, a slimy feel on the reservoir walls or tubing adds to the case.
   • Measure reservoir and root-zone temperature at the end of the light period. Measure the solution in the reservoir and in the root chamber or bucket, at the warmest time of day. Target 18-22 °C (64-72 °F). Above about 23-24 °C (73-75 °F), dissolved oxygen falls and Pythium risk rises; below 16 °C (61 °F) uptake slows.
   • Dissolved oxygen check. Measure DO with a meter in the root zone, or check the system: air pump running, stones bubbling evenly, return water splashing, no dead spots. Target 6-8+ mg/L. Without a meter: if stones are clogged or the pump is undersized for the volume, assume low DO.
   • Send a sample to a plant diagnostic lab. For rots, wilts, leaf spots and viruses you can't separate by eye, send a fresh sample (whole plant with roots or a wilting branch with healthy and diseased tissue) in a sealed bag to a university or commercial plant diagnostic clinic. Results in days to 2 weeks.

Look for

Lower stem and crown with bark scraped back; reddish-brown or dark sunken areas..